The Guardian has recently had a poll for best geek novels of all time (from 1932, which rules out some potential authors in Verne, H.G. Wells and Arthur Conan Doyle - yes I'd class Sherlock Holmes as being definite geek books). This made me think, not least the fact I'd read almost everything in it, apart from Consider Phlebas, American Gods and the Illuminatus trilogy. I have read other books and comics by Iain Banks and Neil Gaiman, but it's a bit surprising considering that I've played the Illumniatii games from Steve Jackson Games many times that I haven't read the trilogy. Fnord.
I found that the discusssion was interesting - and pointed me towards certian authors I've neglected (John Brunner, for example). The genre of 'geek novels' spans both SF, fantasy, 'literature' and other genres. For example I'd argue that Thomas Harris' novels like The Silence of the Lambs is pretty geeky for the ways that research is dropped into the text in a similar fashion to Neal Stephenson's later novels. Microserfs by Douglas Coupland is a novel about geeks, rather than necessarily being about the usual geek obessions. Though coding does feature as a part of the characters professional lives, but the main Coupland themes of the Generation X lifestyle are the novel's main features.
I'd be hard pressed to name a top 20 quickly and will return to this at some point in the near future.