saving graphs; jpeg(), bitmap()

As of Apple's X11 - look in Applications -> Utilities and there 
should be X11. But XDarwin and other X11 are usually mutually 
exclusive, so I doubt that you have Apple's X11. I have no idea why 
someone would install XDarwin instead of Apple's X11 nowadays, it 
makes no sense to me, but maybe someone can explain that.

my guess was that he had 10.1 or 10.2 with Xdarwin, then upgraded to 
10.3. this could result in 10.3+XDarwin.

Hmm.. for 10.2 there was the Apple beta already, but you're right, a 
much-updated system may have XD for historical reasons - but I'd get 
rid of it asap :P. On the other hand, supposedly fink is installed, 
too, but fink is incompatible across versions, you can't upgrade, you 
must re-install, so it seems like a quite messed up system to me ;). 
Ah, well, wait for Tiger, that should make fink obsolete even for 
Bioconductor ... (hopefully...) ;)

mostly xdarwin binaries seemed to die, at some point, though... there 
was some kinda timeout built into at least some versions of it.

Yes, it was more a hack than stable platform - but up to 10.1 you had 
no choice ... I especially hated the WM - it didn't cooperate well with 
other windows and in general copy/paste was a pain... I don't miss that 
:P

Cheers,
Simon