Typing at a standing desk is comfortable if you get the height correct for your body. And for me it is important to have a riser at the front of the keyboard, like this [1]. My arms are angled close to 90 degrees, but pointed slightly downward, a keyboard flat on the desk would put far too much stress on my wrists.

[1] http://cdn.asia.cnet.com/i/r/2008/pp/43776845/sc003.jpg