T3 has probably the most representation considering the games its been in. T3, TTT, SF x Tekken, and Tekken Advance along with other small cameos etc. It's his most iconic costume, so I'd generally put it as the 'best' just considering that it's been the main one more focused on.
I always liked the T3 costume given on how it looks like a good mesh of ninja and...other stuff.
T4 looked amazing, even though it ditched all forms of looking like a samurai/ninja with maybe one exception.
Personally, I like his TTT2 costume along with the T3 costume. It's a good blend of his ties of spiritualism and his samurai/ninja concepts, while still looking a bit crazy and awesome.
Deadpool/Hawkeye/Strider Hiryu all day | Yoshimitsu/Raven | Goh'ing to hell since like...a few months ago.
My personal favorites are (in order) T4P1, T3P1, T2P1 Here are some that I think are underrated:
-Nearly equal to the straw hat imo, though I didn't think so at first http://media.comicvine.com/uploads/0/378/741852-9_yoshi_t2_2_4.jpg
-I really like this one; and it gave Yoshi a "shirtless" look to match many other guys http://images1.wikia.nocookie.net/__cb20111007205407/tekken/en/images/e/e1/Cos-yoshimitsu.jpg
-This one was more streamlined than his canon one, had the classic lightsaber, and that awesome flamewheel http://images1.wikia.nocookie.net/__cb20111007205353/tekken/en/images/d/d0/800px-Yoshimitsu_versus_Lars_-_Tekken_6_Bloodline_Rebellion.jpg
I also think that Yoshi's T5 outfit was almost as good and had the potential to be better than his T3 one, but they didn't quite pull it off. I believe the mask is where they botched it a little
Vroom Vroooom! FULL AUTO!!! I sit alone in my four-cornered room, staring at candles.