I suppose you mean transparent png's, because last time I checked IE supported transparent gifs just fine.
For transparent png's the issue is that semi-transparancy is not completely supported. For this there are several workarounds:
- You can use pngfix for transparent png's included into the page via <img> tags in the html. See http://homepage.ntlworld.com/bobosola/index.htm .
- Or, you can do the same thing that pngfix does explicitly, which is using a directx filter to render the image. You'll probably want to go this route for images loaded at run-time (in javascript or set via css). See http://koivi.com/ie-png-transparency/ .
All in all, I've not come across a situation where I couldn't integrate transparent png's into an IE-compatible page. Though sometimes it can be sort of a pain.
And ofcourse, in IE7 transparency is supported correctly, so there's no more need for workarounds. Too bad IE6 is still so widely used.