If you're still suffering from the 10.4.x problem of X11 windows not coming forward after switching, as described in this hint (despite the fact that a fix has supposedly been implemented), here's a simple workaround.
After switching from an X11 app to any other native OSX App (by using Dock or Command-Tab) and then switching back to X11 ... you can bring all of the X11 windows forward by pressing F10 twice. This activates Exposé's Application Windows mode, and forces all the windows to the foreground.
[robg adds: X11 seems to be working fine on my machine; all windows come forward if I use Command-Tab or the Dock to switch back. If I click on one window, only that window comes forward, as is the case with traditional OS X apps. If you're having the problem after Command-Tab or a Dock click, though, this is a simple workaround.]

