I liked Gundam Wing the most but I didn't understand it too much when it was on... Gundam Seed's characters kind of scared me because they were all crazy and needed meds or something. Oh, and who can forget G Gundam? That was a freaking awesome show right there. Actually, G Gundam's probably more of my favorite than Gundam wing just because I was old enough to understand it when it was on toonami.
Any way, my actual favorite gundams are:
Epion, Heavy Arms, Mercurial, Wing Zero, Burning Gundam, Death Scythe, Dark Gundam, Astray (or whatever the heck that gundam is with the katana from seed), and the regular old zakos (The blue ones with spikes and a beam axe are the cooler ones, though).