I've worked on a heterogeneous system before. It's a commercial system to manage study abroad programs for large universities, and they had installations on Oracle, MySql, and Sql Server. I was an outside consultant handling a very specific conversion project, though, so I didn't get to see many of the issues involved in making it work well everywhere.
I do remember that the single biggest hurdle I had to deal with was Oracle's lack of a simple autoincrement-style column and having to set up separate sequences instead. There were a number of datatype mismatches as well, but there was a pretty good system in place to just map those.
Note that even here, each customer only had one kind of database. We didn't have to worry about replicating data itself between db types (aside from a few common lookup tables). Just structure.