On David's hint, here:
http://www.codeweavers.com/compatibility/browse/name/?app_id=6730;forum=1;msg=109641
I tried installing MSHTML 7 into the same bottle as STO, but still was not able to overcome the "oops" error on launch. I then (keeping with his line of thinking) added "UseGLSL"="enabled" to
HKEY_CURRENT_USER/Software/Wine/Direct3D
in the Start Trek Online bottle. The combination of the MSHTML 7 rendering engine (which brings back the annoying "flicker" in the launcher) and the enabling of the UseGLSL registry key gives me a working install of STO on both my Fedora 15 machine and my Mac OS X 10.6.8. W00t! as it were.
To clarify - you'll find the "Microsoft HTML Rendering Engine 7" in the "Community Supported Applications" section of Crossover Games' Install Software menu. Go ahead and install that into the same bottle as STO.
To apply the registry key, go to Crossover's Run Command menu (which is under "programs", on the Mac), and then select the Star Trek Online bottle and type "regedit" in the command field. In the editor that opens, navigate to
HKEY_CURRENT_USER/Software/Wine
add "Direct3D" as a new key under "Wine", and then within "Direct3D" add "UseGLSL" as a string value, modifying the value to "enabled". Close regedit, and try launching STO. The launcher will flicker horribly and annoyingly, but the game should ultimately launch and work. Exiting the game is a bit unstable under this configuration, which we'll be working on for the next "point release" of CX Games.