Good post from Apple about preparing content for the iPad in particular (but is good to keep in mind for most smartphones and touch-based-devices:
I always spend a few hours working on sprucing things up for the iPhone, at least, and hopefully soon I'll be able to test on an iPad as well :-)
The big gotcha is HTML5 video. There is a cool player called SublimeVideo from Jilion, but IE support is nil, without the Chrome frame installed. FF, Opera, Safari, Chrome, etc. work great, though. Perhaps we'll get a good solution where the site falls back to flash if using IE 6, 7 or 8.
For now, though, I make sure everything besides Flash works well on the iPhone/iPad OS.