I use both PowerPoint 2004 on my Mac and PowerPoint 2003 on a client's Wintel box. While I prefer the Mac version for its more polished Presenters Tools (and ease of using them) and broader selection of slide transitions, I find I prefer the Wintel version's means of managing the Custom Animiations, or slide builds. The Wintel version lets you interact more with the slide, while the Mac version opens a new window, limiting your access to the original slide until you close the window.
I would like to give this feedback to Microsoft so they can address it in the next version of Office (2006?), but their web site is next to useless for giving product feedback:
http://www.microsoft.com/mac/contactus.aspx
If any MS employees troll this forum, please pass it along to the appropriate developers.