Chrome and Safari prompt you (at least on OS X, not sure about others) which certificate you want to use if there are multiple matches.

The bad thing is that it remembers what certificate you want to use and logging out and loggin back in doesn't ask you what certificate you want to use :-(

I've had this issue with the fact that I have two CACert accounts (due to not remembering I had already created one before) and I just recently moved all domains to the newest account...

The browser could ask you which cert to present, but as the saying goes, now you have N problems.