We're on our way to adopting agile practices here at Directi. I being on the UX side of things, know how a lot of usability related things get pushed out of the process because we want to be agile. For some reason, it almost seems like people think agile means FAST?.
Having said that, I think we're doing far more than most software companies do. I'll try and share some inshights on prototyping tools, process and methodos we use soon.

Today, Jakob Nielsen addresses a few Issues on this Topic, here is the summary:

Summary:
Agile methods aim to overcome usability barriers in traditional development, but pose new threats to user experience quality. By modifying Agile approaches, however, many companies have realized the benefits without the pain.

http://www.useit.com/alertbox/agile-methods.html