If I want to give a reference to a physical book, because most references are done to the collection in google books and the sort. What do i do? I have the ISBN no. Is that enough for a citation?
Yes you can give a reference to the physical book and yes it's enough for citation! Just add ISBN, Author's name, Year and Page number, in most cases it's enough. You can do this by clicking on the "Cite" link in edit mode and selecting "Book" from the "Templates" dropdown.
While citing references to a particular website, does the website need to be a reliable one? I went through the tutorials on references and citations, but I couldn'y figure out whether some of the websites I referred to were up to Wikipedia standards.
Yes, while citing references to a particular website it should be a reliable one, and by reliable one I mean any Government/Newspaper/Magazine website are highly recommended.
What is the difference between a Reference and an External Link?
References are used for citing the facts and provide a verifiable source, whereas External Links are used to facilitate "external resources" for e.g., official website related to article. So whenever you are using a fact we should add a reference for it! External Links are mostly optional. You can explore more on this at following links: WP:REF and WP:EL
