So far it sounds like a tie between Storm Shadow and Alley Viper (both first versions). I can respect that.
My second favorite, don't know really off the top of my head. Just know I've always placed Alley Viper in the front middle of my display shelves. Headhunters are cool, so are Vipers as well as Storm Shadow.
I think a good question is who's your favorite Cobra Character. Doesn't have to be the mold but the character from the comics or cartoon. For characters I'd say Major Bludd. He never got sucked into the whole "Hey ninja's are cool, lets make him a ninja now" like they did to Firefly, Snake Eyes, Flint and Road Pig (!?!).
I'd also say the character I've made the most customs of is again Major Bludd.