I use Apple's X11 on Panther to run a range of UNIX apps, including the EMBOSS package for DNA sequence analysis. I like running X11 rootless, so I dont have to keep jumping from Aqua and back. The problem I have encountered is this: Exposé seems to be ignorant of the windows opened by kaptain, which is a system for providing X11 GUI's for working with otherwise user un-friendly command line apps (such as all of EMBOSS!). When I hit the F9 or F10 buttons, the EMBOSS windows fade away, as if they were part of the background ... which is a bit confusing.
My answer is to use a window manager like wmaker or blackbox. Seeminly, they handle the EMBOSS windows perfectly and Exposé treats them like normal windows. Phew.
Problem: when using non-Apple window managers in rootless mode, new windows (like xterms etc) tend to open underneath the Aqua menu bar at the top of the screen. This is a pain, as you can't reach the Close button. However, if you use wmaker, you can fix this as follows. Find the configuration file (~/GNUstep -> Defaults -> Windowmaker) and edit the lines to read as follows:
WorkspaceBorderSize = 22;
and
WorkspaceBorder = TopBottom;
This will stop windows being opened under the Aqua menu bar, and you get the added bonus of being able to use the WMaker dock - which is just like the Aqua one, but can be set up to launch S11 apps.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040710114033251