I don't know if it's just me, but it seems like there are fewer online references for osteology and zoorchaeology than there were back in the 90s when I was an archaeology student. That said, I have found some really great sites for bird osteology.
The first site I found is the
Bird Skull Collection. It's maintained by the Experimental Zoology Group of Wageningen University and is, as the title indicates, a collection of bird skulls, all photographed from multiple views. Obviously, not every bird species in the world is included here, but the collection is vast and continually growing, and the images are clear. In addition to the skulls, there are full skeletons for some species, and even a selection of 3D images. There's even a quiz so you can test your knowledge of bird skulls (I'll leave that for when I've brushed up my skills a bit).
The links page on the above site then led me to the
Seabird Osteology Pages, another site from the Netherlands. The images are mostly skulls, but the scope has expanded to include other bones, too. It's a less comprehensive page than the Bird Skull Collection--as it must be, focusing only on seabirds--but the quality of the photographs is top-notch. So if you're interested in seabirds, this is an essential site.
As for books, the main reference still seems to be
Avian Osteology by B. Miles Gilbert (
buy from amazon). A promising-looking book I haven't actually got my hands on yet is
Manual for the Identification of Bird Bones from Archaeological Sites by Alan Cohen and Dale Serjeantson (
buy from amazon). Another useful reference, especially if you're also interested in tracking and observing living birds, is
Bird Tracks and Sign by Mark Elbroch (
buy from amazon). It's got a decent section on bird skulls, but is limited to North America.
There are also assorted smaller sources and monographs on specific topics. One such is
On the Osteology of the Striges. [Strigidae and Bubonidae] by R.W. Shufeldt (
buy from amazon). It's a reprint from the
Proceedings of the American Philosophical Society from 1900. It's got illustrations of varying utility, but I haven't read it yet, so I can't say how good the text is. I've slowly building an osteology/zooarchaeology library for some time (emphasis on "slowly"), and I'll mention new books as I find them.