If you have Panther (10.3) and are upgrading to Tiger (10.4), an Upgrade install won't hurt anything. I upgraded from 10.4 to 10.5, and the process was absolutely flawless. Most of my settings were intact. The only ones that weren't were new settings introduced in the new OS.
If you ask me, the upgrade process is much cleaner than a windows upgrading process. When dealing with windows, the best thing always seems to be clean install. Upgrades result in reduced performance. Repair installs result in reduced performance. System restore results is reduced performance... This doesn't seem to be the case with upgrading OSX, though.
So if you're doing an upgrade from Panther to Tiger, upgrade should work flawlessly. If you're downgrading from Leopard to Tiger... I don't think you'll be able to select "upgrade" anyway.