The flood follows Halo CE, but the others work around/before the games. Though it is widely considered that the flood is the worst book just because it is so strictly following a game.
The fall of reach mostly takes place in the 40 years prior to halo CE, first strike closes the gap between halo CE and halo 2, halo ghosts of onyx takes place both before halo CE and during Halo 2 and 3. Contact harvest takes place 27 years before Halo CE, when first contact is made with the covenant.
And the latest (and perhaps the best Halo book yet), Halo: Cryptum is the first in a 3 part series that details how the forerunners ultimately activated the Halo rings.
[Edited on 06.02.2011 4:29 PM PDT]