That's easy, the FTB Wiki has a comprehensive list of all bee species (Extra Bees and Thaumic Bees included) and how to breed them.
You should aim for a stable Imperial line for producing Royal Jelly to make parts for Aveieries(sp?), as those have the best production rates for all bees, along with useful components to add to the multiblock structure. Beyond that, whatever end products you're looking for, and any desired traits you wish to cultivate.
I used to do a fun mix of seasonal Leprodine and Tropical bees for good Meadow-like bees to get Silky Combs from. Stung like the dickens, though.