Well, lots of problems with that. You can't virtualize the copy of 10.6.8 that came with your computer for two reasons: First, only retail versions of OSX (not the ones that come with the computer) can be virtualized under the EULA. Second, only server versions of 10.6.8 can be virtualized under that particular EULA (that one changed with later versions). You can purchase a copy of 10.6.8 server edition from apple over the phone for around $20 (or at least you could a few months ago, but you may not want to upgrade the host OS and have all the server baggage running.
You could just download the 10.9 installer and create a new clean VM from scratch, but there's a couple of other challenges: Fusion 3 doesn't support virtualizing 10.9. You'll have to upgrade, and later versions that do, may not run on 10.6.8. It's also probably an EULA violation to virtualize 10.9 on 10.6.8 (even server edition), and it may not even work if your machine doesn't support 10.9 natively. You also may run into issues if you have a Core 2 Duo machine (most 10.6 vintage machines are like that) - since it only has two cores, and 10.9 VM's require 2 cores to function properly, you'll be starving the host for CPU cycles.
Since 10.6.8 is outdated and no longer supported by Apple (not even security patches - so you're at high risk on the Internet), one potential option is to upgrade the host OS to 10.9 (again, assuming that the machine can be upgraded), upgrade to Fusion 6 (or 7 which will be released shortly), buy the 10.6.8 license from apple, and create a 10.6.8 virtual machine (which should have only one core) for those old programs you don't want to update.
Otherwise, the only real option is to dual-boot from an external drive or partition the internal disk - one partition for 10.9 and one for 10.6.8 and boot back and forth between them. That one you can do with the client license of 10.6.8 that came with your machine. But make sure you have a very good backup - and not time machine (it was notorious for silent corruption in pre 10.7 versions, and doesn't backup VM's well at all). I recommend Carbon Copy Cloner from www.bombich.com to make a full clone. You could even clone the machine to an external drive, then upgrade that clone to 10.9 (assuming other software licenses aren't violated with two installs of course).
