I'm open to correction on the following, but here's my understanding of it.
PRAM is supposed to contain only some very basic startup information, startup sound, time zone, etc. But the suspicion is that quite a few software makers either put stuff directly into PRAM or else hook into it to control how certain processes are initiated. It is known that software installs often mess up some setting or other in PRAM - you'll do an install, reboot, and your computer never gets past the gray apple screen for no apparent reason. You zap your PRAM and everything then boots up normally.
Sometimes it's hard to figure out exactly what messed things up, though, because with OS X you generally just need to put the computer to sleep when you don't need it (as opposed to shutting it down). So you might not know that your computer isn't booting correctly until you install an upgrade from Apple that requires a reboot.
