Quoting sander-martijn lists@severeddreams.com:
Because as Ivan said (this is assuming you want to migrate one or some of the sites not all) you would need to use a script like sed or manually separate the tables with the appropriate prefix from the rest of the databse. You might be able to export foo_% but I didn't think using the % variable worked on tables - I could be mistaken.
I think maybe the dba module [1] could use some love to add an export function. The tables for the site would then be Drupal controlled which gives the benefit of not dealing with tables from other sites. It will already do a backup for you but from cron.php.
either way, that's just one of several reasons given why a single database can be more complicated and less desirable than separate databases - however no one said it can't be done and if the benefit outweighs the drawbacks mentioned you certainly can do it, just that there are reasons why it is not the best way to go.
Of course, but the more databases the more database processes you also have so you also need to concern to the CPU power and memory limits of the host.
[1] http://drupal.org/project/dba
Earnie -- http://for-my-kids.com/ -- http://give-me-an-offer.com/