I doled out a bunch of upvotes for other users, but just to give my two cents the only three annotations I use with any regularity in development are the main annotations used directly by the compiler:
@Override - Great for making it explicit in your code when you're overriding another method. Also has the extra benefit of being flagged as a compilation error if you don't override a method the way you think you are (see this other SO post). This flag informs the compiler that you're intending to override something, so if you don't (e.g. you forget an argument in the method signature), the compiler will catch it.
@Deprecated - Indicate whatever you're marking as something that should not be used from this point forward. The compiler will generate warnings for use of any code elements you've marked as deprecated. In general, deprecation says "this was in here in the past, but it may go away in a future version." Make sure you also use the associated "@deprecated" Javadoc flag in conjunction with this too to tell people what they should use instead.
@SuppressWarnings - Tell the compiler to suppress specific warnings it would otherwise generate. This can be useful for things like when you intentionally want to use deprecated methods, you can block out the deprecation warning. I tend to use it a lot to block out everyone's favorite "Serialization UID" warning on serializable classes (whether or not you should do that is another debate for another time). Just handy for those cases where you know something you're doing is generating a warning, but you're 100% sure it's the proper behavior you want.
Look at the Sun Annotations Guide and check out the section "Annotations Used by the Compiler". These three are given a fairly lengthy discussion.