Unlike most upgrades, you'll be ripping out the 9x kernel and replacing it with an NT-based kernel. The registry will somewhat migrate over, but there are differences - this can break applications, so backing up your data and installing clean will probably result in the lowest amount of downtime. If any app breaks, or you need to troubleshoot some random upgrade-related problem, the upgrade will cost you more downtime and be more problematic than a clean install of XP and your apps, and migration of data back.