One of the major arguments against dinosaur to bird evolution goes something like this:
"[S]cientists believe that birds descended from theropod dinosaurs. But theropod dinosaurs have lost digits IV and V from a primitively five-fingered hand, leaving them with digits I, II, and III. Birds, on the other hand, have digits II, III, and IV, having lost digits I and V. It is almost impossible for the two groups to be closely related with such a significant anatomical difference."
Biologist P.Z. Myers wrote an excellent article about this a while back and answered this criticism thusly:
"Anatomists initially assigned digit numbers I, II, and III to bird limbs on the basis of their form, but later had to revise that to II, III, and IV on the basis of embryology. Dinosaur digits are assigned numbers I, II, and III on the basis of their adult form (which is admittedly much less ambiguous than adult bird digits!)…but what about their embryology? If we had access to information about expression of molecular markers and early condensations in the dinosaur limb, would we have to revise their digit numbers?"
He goes on to talk about the hypothesis that dinosaur fingers 2,3, and 4 began devoloping as digits 1,2, and 3 due to a mutation in the genes that control development. This was scoffed at by creationists as being a "baseless speculation to try to save the dino to bird theory from reality". Well, now creationists are once again the ones who need saving from reality. Scientists have been doing some work on the gene expression in the alligator (the closest living relative of birds) and have found that a a gene called "Hox D-11" is not expressed in digit 1 of mice and alligators and is also not expressed in the second digit of birds. This means... Dah-dah-dah-dah! The digit 2 in birds is really just digit 1 developing as digit 2. Just what the "baseless speculation" mentioned earlier predicts.
Dino/Bird Transitional Fossils:
The Classic: Archaeopteryx
Sinosauropteryx: The Dino with Protofeathers**
T. Rex Cousin Had Feathers
A Giant Turkey-Like Dinosaur
The '7 Foot Turkey'
Velociraptor Had Feathers
Microraptor: The Four Winged Dinosaur
NOVA: The Four Winged Dinosaur
Bird Fossil Transitions
** I have addressed a criticism of the Sinosauropteryx fossil here.