My favorite overall is not from any anime, but is the Huckebein MkII from Super Robot Wars Alpha.

From anime, GaoGaiGar and Star GaoGaiGar are the top picks for me I think.

I also like the various Aestivalis designs in Nadesico a great deal.

My favorite Gundam mobile suit is the NT-1 Alex. I realize how strange of a choice that is, but it's been the answer for many years and no matter how much I think over it again, I always end up standing by it.

Hi-nu is an honorable mention, particularly the purple accents version.