Let's see.
'Only a Fairy Tale' and 'Not Just a Fairy Tale' are crosses with STTOS (the movies)
'Plane Storm' and 'After the Storm' are crosses with Superman Returns
'Lois and Cl - Kal-El', and 'The Smallville Connection' both cross with UFO.
'What Happens in Metropolis...' is a cross with Frazier.
Coffee at the Bakery, and Bakery Redux aren't exactly cross-overs. But they star the Lois and Clark from Smallville.
And I just realized I had two stories elsewhere that I forgot to submit.