You may wish to check that whether you machine has been overclocked. I just finished battling a similarly confusing set of symptoms. For me I was getting hard kernel freezes correlated with long compiles (kernel, mozilla, XFree86, etc.).
After testing the RAM, swap partition, various kernels, and repeated re-installations I remembered that I had overclocked my 400MHz B/W G3 to 450 a year ago. The instant I reset the jumpers to 400 all my problems went away... Particularly weird since OS9 and OSX are extremely stable (albeit painfully slow) ie. no problems doing compiles of similar length under OSX and Unreal is solid under OS9... That still has me puzzled... Anyway, FWIW, -- Brad