What's the best way to deal with wmv files on iPad
Did you tried Oplayer ?

Didn't tried it with wmv but works perfectly for me on my iPad 1, with mkv and other formats, even with subtitles. I would love to try it on iPad 2 to see if the new CPU handles 720p videos :)

VLC for iOS was promising before it was removed... sigh. :/

Update 2018: VLC for Mobile is available in Apple Store.