I loved the 3 days that I had in Berlin, except that it wasn't nearly enough time.

Here's what I would suggest:
1) Check out the Berlin episode of "No Reservations" (it should be on youtube) for some ideas, and it's got some interesting history as well. There's a deli featured in the show that is a bit out of the way, but I decided to check it out - good food, but a lot smaller than it seems in the show.
2) Also check out HostelWorld's Berlin guide for ideas.
3) If you're into street art and that sort of thing, I strongly recommend the http://www.alternativeberlin.com/ free walking tour that meets at the Alexanderplatz Starbucks (ironically the least "alternative" spot in Berlin).
4) Bundestag - well worth it, even if just for the view from up there, but it is an impressive building in it's own right.

hmmm maybe I should go back!