I've been disappointed in a few. Trigun just because the manga is so much better. Tactics because it left so many of the yaoi undertones that were in the manga out. I still love it, but I miss those undertones, darn it!
Gravitation I have mixed feelings about. It has the wonderful J-pop music soundtrack that makes it awesome
but the manga was so much more detailed and you were able to get a better feeling for the characters. The anime left some characters out and left out the more....intimate scenes.