A bit of testing shows that this happens on Tiger with the Safari 3 WebKit? installed, but a (very) cursory check does not seem to have this happen on Leopard.
Periodically (often right after startup, but sometimes after hours running) Colloquy will begin to eat 95% or more of the CPU. Colloquy itself does not become in any way unresponsive or beachball, but the CPU of the machine is driven to the point that the fans kick in, and top or any other form of process monitor shows Colloquy pegging the CPU. Needless to say, this makes other software turn sluggish!
Disconnecting from everything, closing all windows, and basically making Colloquy stop doing everything does NOT correct this; only an entire quit and restart will solve the problem, and even then a restart seems likely to immediately peg again.