I use ITA to search by fare class.

http://matrix.itasoftware.com/cvg/dispatch/prego

To search for B fares, go to ITA, enter your origin as such:

CLT:: us+ / f bc=b

And the destination as:
FCO:: us+ / f bc=b

Where CLT and FCO are the airport codes, obviously and "B" is the fare class. To search for y fare, you'd enter ....bc=y, for example.

Hope this helps!