The ones which jump into my mind immediately when I think about this are
The Red Riding Trilogy (I'll count that as one choice) by David Peace
Jonathan Strange and Mr Norrell by Susannah Clarke
Blood Meridian by Cormac McCarthy
Cloud Atlas by David Mitchell
Averno by Louise Gluck
Shakespeare's Language by Frank Kermode
Light M John Harrison
Darkmans, Nicola Barker
ETA - I think Beyond Black by Hilary Mantel
There are several other books I liked a lot, and most of the SF I have read is like that - probably not top ten, but really good: Snow, Years of Rice and Salt, Transition, Black Man, House of Leaves, The Separation, Oscar Wao. OK, looking at them and seeing how much I like them, I'm now thinking I probably need to do two top tens, one SF and one 'other' ... No, one Sf, one fantasy, and one 'other'.
Obviously I'm going to have to think a bit more about this. I will post this to my blog anyway, just so I don't forget what I'm thinking about.