There are still a few issues with InDesign that so far Adobe seem reluctant to deal with, although they are well publicised - assuming you're using a Mac, CS3 and Leopard, there are really annoying things like the inability to hide the application to get back to the desktop without having to move the window, every now and again it force-quits itself <hooray for temporary files> and its reluctance every now and again to switch between itself and other applications without having to reboot the Finder.
But that said, I use it now instead of Quark, which I've been using since version 3.3!