GreekBibleStudy - I've used this with my first year greek students. It it helpful for looking up a word and seeing every instance in the NT. This is great for vocab building, especially if you learn the paradigms first, then look up the lexical form of the word and see all of its inflections in use. This site also has downloads of the entire audio Greek New Testament in Erasmian and Modern pronunciation. This is just awesome!
Readers Version - I have not used this much, but it seems considerably faster than the previous website.
Bible Web App - This seems to be a difference version of the Readers version.
Perseus - This isn't just the New Testament, has lots of classical and hellenistic Greek.
OpenText - For what it is, this is helpful.
New Testament Diagrams-This is helpful, but it costs a bit of money. Nevertheless, nice to see somebody else's diagrams in action.
Dr. Decker's Class Helps - Here are some nice things, particularly the .pdf vocab helps.
TextKit - This site has a plethora of awesome resources.
Greek Library Online - This has a multitude of greek texts for your reading pleasure. If you're got the New Testament chops you can get on with reading the Echiridion.
Mike's List of Helpful Resources on google books - These are helpful and free, also his blog is filled with useful information concerning linguistics and greek.
Gervatoshav's Downloads - This is helpful stuff for the new pronunciation.