There's been a lot of comments of that sort showing up. Personally I'm disappointed by the lack of TMNT III, which in my mind is a stellar soundtrack the entire way through. Despite the effort put in to reduce nostalgia bias and cover some of the more overlooked titles, you can see that there's still quite a few entries from the popular titles (the Mega Man and Castlevania series in particular.) I'm not surprised by this, and I can't deny how great the soundtracks are, but I would have liked to see more dark horse titles show up. For example, Shizzie Auriplane pointed out this great track from a really obscure game (Tantei Jinguuji Saburou 4? Has anyone here ever heard of that before?).
That said, I'm really happy to see that Silver Surfer track near the top of the list. Such an impressive track, for technical AND musical reasons. Can you believe that drum sound is composed entirely of the triangle wave and noise channel, and DOESN'T use samples?