I have had many favorite epis but here are just a few (in no particular order)
The Stalker (when nick is stalked)
Fur and Loathing (hehehe people in mascot costumes)
Law of Gravity (Keppler dies, although I wish he didn't)
Shooting Stars (the cult people)
Who Shot Sherlock (one of the best)
Chaos Theory (just love the whole randomness of it)
The Finger (Catherine and the random guy with his girlfriends finger)
The Pilot (Grissom was awsome in the pilot so much funnier and appeared to have more empathy)
I-15 murders (killer truck driver, kinda)
Justice is Served (because it was the first one I saw, and she tried to feed Grissom people ^.^)
Any of the ones with the blue paint killer
Any of the ones with Lady Heather