What most of us do before installing a new OS is to use Carbon Copy Cloner or some other clone app and back up your existing system to another disc (either internal or external), not a partition. That's your fall back to boot off in case you have probs with the new OS.
With that step out of the way and tested. You are then set to either go the upgrade path with the new OS or to wipe your existing boot disc (erase and write zero's) and go the fresh/clean install path. Yeah you have to reinstall all your apps and plugins etc; but at least you can be sure that you have a squeaky clean OS.
I opt for the wipe and clean install method, unless you go buy a spanker new disc and throw tiger on that, not an issue if you're working on a tower. On my PB I'll have to clone off to a FW drive, boot off that - wipe the internal and then install tiger.
Hope it helps, cheers
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