Separate DB
 

Should I use a separate db for each blog domain I set-up?

Advantages to seperate DBs: (As I see them)

More flexibility (you could do a huge change to one, but not the others)
If one goes down, you have other ones (assuming that one doesnt bring your service down)

Disadvantages: (as I see them)

Updating means updating each database in turn
You can't easily link information together (share links tables etc)

I was a big fan of using a single db, easy to backup. And hell what could happen with my host doing regular backups and me doing regular backups. Shit should have been safe. Keyword should have been.

Now I have seperate databases for everything and keep backups forever.

Use them separately!

Using one database may be easier to back up and update but one corruption and all blogs are affected while using multiple databases may be a hassle to back up and update but it's worth it especially if corruption happens. In that case, only one blog is affected, not all of them.

I also have to point out that nowadays, backing up and updating your blogs are made easier with plug-ins that do them automatically for you.

My take is that it really depends on Your server resources ... too many DB's can slow Your server down (happened to me) once it hits a loot of traffic (though cashing pages might help and keep overload down).