The 10.6.3 white retail disk (so called "upgrade disk") sold online at Apple are full version disk of OS X Snow Leopard, however it also has a upgrade installer for OS X versions 10.4 and 10.5.
So if you boot the Mac into 10.4/10.5 and stick the DVD in and double click the upgrader, it will replace 10.4/10.5 with 10.6.3 and leave your programs and files alone.
If you stick the same disk in and boot the machine while holding c or option/alt key down (wired/built in keyboard) you get the opportunity to use Disk Utility (and others) and can erase the entire drive and then install OS X 10.6.3 Snow Leopard fresh. However this disk is sans-free iLife, but can be reinstalled via the 10.5 machine disks.
I don't know the specifics of the full version of the Snow Leopard install disks as I never used them, or what particular advantage they have (free iLife?), but if it requires a erase and install, then that's a disadvantage obviously as you can't carry over your already installed 10.5 programs.
OS X 10.4/10.5 need to upgrade, 10.6.8 ok still
How to erase and install Snow Leopard 10.6
Restoring your Free iLife (iPhoto, iMovie etc)