From the apache conf you posted, it looks like you just need a couple of domains aliased to one account, that is easily done, this does however mean that everything about these domains will be aliased mail, web, ftp, ....
For example if you have
bill@domain.com, then you will also have
bill@domain2.com, and all emails will be collectable from a single pop box, instead of 2 different ones.
Aliasing doesn't automatically mean that the aliases will be forwarded to the main domain but that could be done with a simple htaccess rule but I don't think thats what you want.
depends how much these sites share, but it sounds like it could be possible, how do you normally work the email addresses? are they independant, or would it be ok to share the pop3 mailboxes?