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
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
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