It is very difficult to merge the portals from separate databases into one database. You cannot just copy the records from one into the other, because the ID numbers of various records will be the same in both databases. For example, you may have a page in database A with TabID 200 and a completely different page in database B also with TabID 200.

The best method will be to export each portal to a template file (using Host menu>Portals page) and then create a new portal from the template file (also using Host menu>Portals page). However you will loose details doing this - some module types will not be included, and your users will not be included. Note that you have to have the same version of every module installed on the 2nd server as you do on the 1st.

I guess it does happen, but not enough for someone to build a tool to do it!

Regarding the users, there are several "bulk-import users" modules on snowcovered.com. There may be one to transfer users from one DB to another. If not you could write a SQL query to extract the user details from one DB into a file, then use the import module to import them into the 2nd DB. Because you cannot get the passwords out in clear text, I would look for an import module that assigned each user a random password and then email them all their password.