Well,although you can find a lot of Trigun music videos,my favorite are those two:
This Is Living by Sierra Lorna The song rules and fits perfectly with the theme of Trigun and the life of Vash,the effects used are very good and the synch is perfect.It is basically an action music video and has shots of every major character,although it relies on Vash.A must download for every Trigun fan.
Eden Remastered by Hakura It's one of the most dramatic music videos ever made.It can make you cry,really.Not a lot of effects,basically fades but a decent work which has received many opinions and really deserves a lot more.And the meaning at the end is the best above all.
I think the best Trigun video I have seen is Nowhere Man by LavaLamp. Since there are so many Trigun videos out there it is great to see one where someone doesn't use the same clip of Vash dancing over and over again. The song is also very fitting for Trigun.
This is my favourite Trigun vid, first shown at AyaCon 2005, and in my opinion, the best video there. It hasn't got flashy special effects, but when a video has a much feeling as this, who needs gimmicks?
I have to add the best Trigun video I've ever seen! Stumbled apon in an attempt to find videos for clips, I found TriEngel a video to Rammstein-Engel. I give it a 10/10. You should check it out and see for your self.