The 92A1 is the newest version of the 92, the next step after the 92FS, I can't go into details as its been a while since I looked into it, but the 92A1 features some improvements that were needed in the 96, which is the 40 S&W version of the 92. I think the main differences are the addition of a "Buffer", and of coarse the rail on the dust cover. I think that's about it really, although like I said its been a while since I looked into it.
the "M9" is just the US military version, it has a two dot sight rather then the standard three, and I think the grip is a little different. I have not seen an M9 style pistols new up here in a while, so its a non issue in my opinion.
Honestly, the 92FS is probably the best option, cheaper, and has those classic line that made the pistol a classic. And unless your going for the 96, the above improvements are lost on the 9mm.
Related note: If you want a budget "92", the Turkish made Girsan (Right spelling?) pistols are a few hundred dollars less, and form what i have been reading, are every bit as good as a Beretta.