Coelophysis (late Triassic) -- One of the first theropod dinosaurs. Theropods in general show clear general skeletal affinities with birds (long limbs, hollow bones, foot with 3 toes in front and 1 reversed toe behind, long ilium). Jurassic theropods like Compsognathus are particularly similar to birds.
Deinonychus, Oviraptor, and other advanced theropods (late Jurassic, Cretaceous) -- Predatory bipedal advanced theropods, larger, with more bird-like skeletal features: semilunate carpal, bony sternum, long arms, reversed pubis. Clearly runners, though, not fliers. These advanced theropods even had clavicles, sometimes fused as in birds. Says Clark (1992): "The detailed similarity between birds and theropod dinosaurs such as Deinonychus is so striking and so pervasive throughout the skeleton that a considerable amount of special pleading is needed to come to any conclusion other than that the sister-group of birds among fossils is one of several theropod dinosaurs." The particular fossils listed here are are not directly ancestral, though, as they occur after Archeopteryx.
Lisboasaurus estesi & other "troodontid dinosaur-birds" (mid-Jurassic) -- A bird-like theropod reptile with very bird-like teeth (that is, teeth very like those of early toothed birds, since modern birds have no teeth). These really could be ancestral.
GAP: The exact reptilian ancestor of Archeopteryx, and the first development of feathers, are unknown. Early bird evolution seems to have involved little forest climbers and then little forest fliers, both of which are guaranteed to leave very bad fossil records (little animal + acidic forest soil = no remains). Archeopteryx itself is really about the best we could ask for: several specimens has superb feather impressions, it is clearly related to both reptiles and birds, and it clearly shows that the transition is feasible.
One possible ancestor of Archeopteryx is Protoavis (Triassic, ~225 Ma) -- A highly controversial fossil that may or may not be an extremely early bird. Unfortunately, not enough of the fossil was recovered to determine if it is definitely related to the birds.
Archeopteryx lithographica (Late Jurassic, 150 Ma) -- The several known specimes of this deservedly famous fossil show a mosaic of reptilian and avian features, with the reptilian features predominating. The skull and skeleton are basically reptilian (skull, teeth, vertebrae, sternum, ribs, pelvis, tail, digits, claws, generally unfused bones). Bird traits are limited to an avian furcula (wishbone, for attachment of flight muscles; recall that at least some dinosaurs had this too), modified forelimbs, and -- the real kicker -- unmistakable lift-producing flight feathers. Archeopteryx could probably flap from tree to tree, but couldn't take off from the ground, since it lacked a keeled breastbone for large flight muscles, and had a weak shoulder compared to modern birds. May not have been the direct ancestor of modern birds. (Wellnhofer, 1993)
Sinornis santensis ("Chinese bird", early Cretaceous, 138 Ma) -- A recently found little primitive bird. Bird traits: short trunk, claws on the toes, flight-specialized shoulders, stronger flight- feather bones, tightly folding wrist, short hand. (These traits make it a much better flier than Archeopteryx.) Reptilian traits: teeth, stomach ribs, unfused hand bones, reptilian-shaped unfused pelvis. (These remaining reptilian traits wouldn't have interfered with flight.) Intermediate traits: metatarsals partially fused, medium-sized sternal keel, medium-length tail (8 vertebrae) with fused pygostyle at the tip. (Sereno & Rao, 1992).
"Las Hoyas bird" or "Spanish bird" [not yet named; early Cretaceous, 131 Ma) -- Another recently found "little forest flier". It still has reptilian pelvis & legs, with bird-like shoulder. Tail is medium-length with a fused tip. A fossil down feather was found with the Las Hoyas bird, indicating homeothermy. (Sanz et al., 1992)
Ambiortus dementjevi (early Cretaceous, 125 Ma) -- The third known "little forest flier", found in 1985. Very fragmentary fossil.
Hesperornis, Ichthyornis, and other Cretaceous diving birds -- This line of birds became specialized for diving, like modern cormorants. As they lived along saltwater coasts, there are many fossils known. Skeleton further modified for flight (fusion of pelvis bones, fusion of hand bones, short & fused tail). Still had true socketed teeth, a reptilian trait.
