We run mostly express as this is sufficient for sites with less than 300 clients and the usual load (software deployment, imaging a couple of clients per day). Larger sites have the db stored on a SQL cluster (increases performance heavily !!!), which from our experience is the best approach as there the load is also much higher due to the managed nodes.
Hope this helps?
SK is dead on and frankly has loads of DS 6.x experience.
The key is the scale of YOUR deployment: # of nodes, how often you're re-imaging, how many PXE/Sites you're managing, etc. DS 6.9 has a flat DB format and is NOT a heavy DB hitter, unless you really scale it up (especially as compared to the SMP). So as a general rule, customers have been, as SK said, very happy with SQL Express. If you find you're in a larger environment, it's likely worth the cost to just do it right the first time.
Other DB instances on the same DB server? Again, depends on scale. For DS 6.9 you're not seeing heavy access, large reports, etc, so it'll share, but on SQL Express that's stupid, frankly. With a separate server though it can easily share.
We use SQL Express with over 120 Pxe servers. We deploy over 5000+ clients a year.
We have not experienced any performance issues.
Very happy about DS 6.9 SP6