I was almost positive that I posted in this thread before, but I guess I didn't. Anyway, I'm a big fan of both of those shows, but Trigun's superior in terms of my liking of the two.
Gundam Wing scores big points in my book because it was one of the shows that really got me into anime. It's also my favourite in the Gundam series (though SEED comes close). I'm a big fan of how political the series is. With regards to favourite Gundams, I always liked Epyon the most. The third Talgeese was cool, as was Dethscythe and its various forms.
With regards to Trigun, about which I'll avoid ranting, Wolfwood is my favourite character. Although Vash is ridiculously cool, Wolfwood's character just makes me very, very happy. I love him >_<. Needless to say, the ending of the series...well, you get the picture. Both are great shows!
