Keeping your Windows system secure and running like a well oiled machine requires regular maintenance and judicious use of drive space. Be careful to only run executable files that come from trusted sources, and never keep software that you do not use regularly. Always ensure software does not start with Windows unless you wish for it to be running at all times. Regularly examine running processes and services using task manager or Process Explorer and services.msc. Process Explorer is a great improvement on task manager's process tab and it can be downloaded for free from Microsoft. Services.msc (run as admin) is built into Windows and grants more control over services than task manager.

I have selected at least two recommendations for every utility type except where there is an undisputed best that also happens to be free (or if my experience is limited--there will be updates). For most of these you can use two, but it would be redundant and wasteful. It is a bad idea to use two anti-virus or two VPNs because they may compromise each other. Multiple firewalls will just cause a huge annoyance.

System Maintenance

System Cleaner

Over time your system will accumulate a lot of clutter that should be cleaned. Avoid tuneup software with farfetched and too good to be true claims that they fix everything, those tend to cause more issues than they solve. These two, however, are very good.

 -CCleaner + CCEnhancer (freeware): Advantages include an attractive and easy to use interface, a variety of features, registry cleaning, and CCEnhancer helps cleaning the junk from many third party programs.
 -Bleachbit (open source): Simple cleaner only that ignores most third party software, but it seems to do a deeper clean of core programs' mess than CCleaner.

> Drive management: Manage partitions and keep your disks healthy. Find and repair bad sectors, file system errors, and keep drives aligned properly.

 -Paragon Hard Disk Manager ($50 - $100 Suite vs Pro). Advantages include a wide variety of features normally covered by dedicated pieces of software such as data backup and recovery, virtual drive management, and drive cloning.
 -AOMEI Partition Assistant Standard (freeware). Disk and partition management is comparable to Paragon, but it has little as far as extra features go. EaseUS is supposed to have a comparable partition manager, but I have only tried their recovery software so I don't know how it compares.

> Backup & Recovery: Keep your data safe in the event of drive failures.

 -Acronis True Image ($50): This is a great backup & recovery suite that does everything you would need for data backup. I particularly like incremental backups to keep my backup up to date without wasting huge amounts of time on each backup.
 -EaseUS Data Recovery (free, $70 or $100): This is a nice recovery suite. Rather than focusing on proactive backups, this software is a last resort to pick find deleted files even on unrecognizable or reformatted partitions.
 -Piriform Recuva (freeware): This is a great free tool similar to EaseUS. It is limited in comparison to the the paid version.
 -TestDisk & PhotoRec (freeware): Said to be the best free recovery software, but no GUI. Command-line only.

> Uninstaller: Proprietary uninstallers leave a mess behind. Use a dedicated uninstaller program to do a better job of keeping your computer free from bloatware.

 -Revo Uninstaller ($40): Advantages include a variety of system cleaner options, and installing software with Revo logs installations to ensure they can be totally removed.
 -Comodo Programs Manager (freeware): Advantages include management of drivers, services, and Windows features and updates. These can all be done in Windows but Comodo puts them in one place. Warning: starts at boot and runs in background at all times unless disabled manually.

> Disk Defragmenter: Only defragment HDDs. There are many third party applications that do a better job than Windows.

 -Diskeeper 12 ($30 - $65, Home vs Pro) Many features for active fragmentation management and avoidance. Diskeeper 12 brings new features unseen in 11 to help manage SSDs, but you should be careful regardless because software like this still tends to over-manage SSDs. SSDs are good at managing themselves. Warning: starts at boot and runs in background at all times unless disabled manually.
 -Puran Defrag (freeware): Most features that can be found in free defragmentation software. Warning: May start at boot and run in background.

II. Security: Lightweight but effective security software is key for keeping your PC performing well.

> Web Browser Security: Ensure you are browsing the web safely. These are Chrome extensions, but similar utilities can be found for other browsers.

 -WOT: This extension gives you a safety rating of every website you visit and allows you to read and write reviews. If you try to visit a poorly rated website it will warn you before granting access. This extension puts a logo with varying colors based on the rating of a website next to every Google search result.
 -HTTPS Everywhere: This extension ensures that you always use SSL if it is available, and asks permission before running insecure scripts in an SSL page.
 -Javascript & Plugin settings: For the safest possible browser experience, ensure that javascript is disabled (you can whitelist individual websites as you browse the web) and set plugins to "click to play."
 -Adblock: Do not use Adblock Plus, they are paid by advertisers to let some ads through.

> Windows Firewall Controller: Windows has a strong firewall, however its interface is poorly designed and has limited management options. Use a third party controller to make it as good as any paid firewall.

 -Tinywall (freeware): Minimalist context-menu-based interface and convenient and easy to use configuration features such as "whitelist by window" and autolearn. Can be used effectively without ever accessing the settings window. Tinywall is a rock solid non-invasive firewall that blocks everything by default with no notifications. This lends itself to extreme security unparalleled by the vast majority of other firewalls. The only security advantage a select few firewalls might have is if it comes with HIPS protection. Other non-firewall software does have HIPS protection available, such as ESET NOD32 Anti-Virus.
 -Binisoft (freeware): Fewer features and more resource intensive than Tinywall (but still very lightweight). User friendly GUI that places all of the tools in one tabbed window. Notifications available for paid users.

> Anti-Malware: It is valuable to guard against malware with both a strong anti-virus and also specialized anti-malware software that stays up to date to protect you against a wide variety of rapidly evolving non-virus malware. Certain anti-virus software (especially security suites) tend to be very invasive and hurt performance. Sometimes I feel like they are as bad as the malware they are meant to prevent. Low resource consumption should always be a key consideration here. Warning: all of these start at boot and run in background at all times unless disabled manually.

-ESET NOD32 Antivirus ($30/yr): Best combination of light resource usage and anti-virus. About the same security level without the bloat when compared to the paid software mentioned below. HIPS protection works well together with TinyWall to prevent firewall exploits. Heavier than the freeware but also better protection.
-Free: Microsoft Security Essentials, Avast, AVG, and Bitdefender Free (not Plus) are all lightweight and unobtrusive with good anti-virus capabilities.
-Malwarebytes Anti-Malware ($0 - $25): The free version is limited to only scans, while the paid version has active malware prevention tools. Both have no real competition when it comes to non-virus malware protection. Because it is so specialized, it should be combined with specialized anti-virus software. Some all encompassing security suites may interfere with Malwarebytes.
-Paid: Bitdefender Plus, Norton, or Kaspersky: These three are often cited as having the best overall protection, and they are loaded with plenty of anti-stupid features to keep you from making obvious mistakes. They are very resource intensive and sometimes get in the way of normal PC usage. I personally do not recommend this kind of software (McAfee and ZoneAlarm fit in the same category) because they will most likely not make any difference aside from irritating you. If you like being irritated for the sake of negligible security improvements, they are worth your consideration. For any of these I would recommend getting the plain anti-virus version, not a full security suite.

> Cryptography: Encrypt sensitive documents to avoid identity theft. It is best to use open source encryption protocols.

 -AES Crypt (open source): AES-256, simple encryption of individual files into industry standard .aes files, context menu based. Very easy to use.
 -TrueCrypt 7.1 (not 7.2) (debatably open source): A now defunct project that was in charge of perhaps the best encryption software available. Full disk encryption, mountable virtual encrypted volumes (behave like a drive when mounted), variety of encryption and hash algorithms, hidden volumes (decrypts to one of two things depending on key used for plausible deniability). Wizards make this easy to use if you stick to default options. Available at truecrypt.ch, not truecrypt.org. Despite malicious rumors, TrueCrypt code has proven to compile to the distributed binary and has been audited and shown to lack intentional security weaknesses.
 -Veracrypt (open source): A fork of TrueCrypt with improvements to some of its weaknesses, developed by a private group. Interface is identical to TrueCrypt.
 -CipherShed: Community based open source project currently working on their first TrueCrypt fork release. CipherShed has teamed up with TCNext as a unified project. Ciphershed.org forums are dead, all discussion is at the TCNext website, truecrypt.ch.
 -GPG (open source): PGP based asymmetric key encryption--use key files (save keyring in safe place) with public and private key information for secure communication. Seems strange at first, but easy once you get the hang of it. More for communication than personal data security.

> VPN: A Virtual Private Network can boost your privacy by encrypting web traffic and keeping you anonymous over the web to combat identity thieves and other hackers. I have sometimes found my VPN to actually increase speeds which is most likely due to bypassing WAN bottlenecks and ISP throttling.

 -Private Internet Access ($40/year): Perhaps the best mainstream VPN with a price lower than almost anyone else. AES-256 Encryption, DNS and IPv6 leak protection, kill switch, anonymous payment, shared anonymous IP address, many servers worldwide. In my experience, client PC speeds are usually capable of reaching at least 20 - 50 Mb/s. Warning: starts at boot and runs in background at all times unless disabled manually.
 -OpenVPN + Ramnode VPS ($12/year): This takes a little command line configuration to start, but there are step by step instructions on the web. Setting up your own VPN gives you the highest possible degree of versatility. 1 Gb/s, 500 GB/month (more bandwidth costs more), unique private IP address. To make an anonymous payment to Ramnode, use a pre-paid Visa with dummy credentials.

III. File Management: File management tools do not necessarily improve the performance of the system, but they improve upon the usability of core system tools, so they are worth mentioning.

> File Manager:

-QTTabBar (freeware): This is a great little dll extension to add tabbing to Windows Explorer. It's very simple, but there are a ton of options making it very customizable. I used this for years before switching to a dedicated third party file manager.
-XYplorer ($30 for lifetime updates): Most features by far in a file manager. Dual pane (horizontal and vertical) and tabbed browsing also with an incredibly comprehensive tabbed details/search pane (also horizontal or vertical). The catalog is a great shortcut feature that goes beyond .ink files. The developer is great, I once contacted him about a feature I wanted and the same day he released a new version with precisely that feature. Optional custom highlighting which makes executables, video files, music files, text files, etc. all have their own font color, plus special files also are actually highlighted (eg. recently modified is highlighted green). You can also write scripts for your own custom features. XYplorer has proprietary tools for everything, and each one improves on what Windows has to offer. Great proprietary 32 bit context menu with "rename special" options that change groups of files' names according to certain rules. XYplorer does not support MTP.
-Directory Opus ($50 - $90 for only current version): This is a very nice alternative to XYplorer. It doesn't have quite as many features, but it is 64-bit. Rather than develop their own proprietary tools for everything, they rely a bit more on Windows features that already exist, so it recognizes MTP and uses the normal Windows 64-bit context menu. One proprietary thing that DOpus does have is its own file copier, but it isn't as good as some other third party copiers. While XYplorer has a very ergonomic and utilitarian interface, and both have very modern features, DOpus has a more attractive and modern aesthetic, and toolbars can be moved around a bit more freely.
-xplorer2 (free or $30 for pro version): This is a great alternative to Windows Explorer + QTTabBar, but it is somewhat dated and lacking compared to DOpus and XYplorer. The one advantage it has over those two is that pane placement is much more custom. Anything can go anywhere, and anything can turn into a menu style item (eg. click to bring out the tree as a temporary overlay on the left or right until you click elsewhere).

> File Copier: Improve performance and reliability over Windows copier.

 -TeraCopy (freeware): The most feature packed with above average speed and reliability. Pause and resume copies, verify results, and directly monitor and control which files are being transferred as the transfer is taking place.
 -Fastcopy: The fastest. No special features.
 -Unstoppable copier: The most reliable with decent features but very slow. Data recovery and corrupted file transfer.

> File Indexer

 -Everything (freeware): This indexer works far better than Windows Search. Its service is far less intrusive; it doesn't eat up CPU cycles like the Windows indexer. Also, search results are shockingly instantaneous even on a PC with several drives and millions of files. Make absolutely sure to totally disable any Windows indexing if you choose to use Everything.

> Download Manager: Like file copiers with your OS, these improve the performance of web browser downloaders and give you plenty of features. Never lose another partial download again. Linux distros and Android ROMs are best downloaded via torrents. Remember to seed back 1:1! There are many applications for torrents.

 -Download Ninja (freeware): An excellent brand new feature packed download manager with a simple and intuitive interface. Special features include media download tool for websites like YouTube.com. Very active development. Runs in background by default. Make sure to get the appropriate add-on or extension for your preferred web browser.
 -μTorrent (freeware): Good torrent software. Sometimes there are problems. Some people recommend using a version from years ago and say it has only gotten worse. Do research to find what's best for you.
 -Deluge (open source): Rock solid torrent software with similar interface to uTorrent. Slightly simpler than uTorrent.