Crates are large boxes that can be added as decorations or Story mode objectives in Mapmaker maps in both TimeSplitters 2 and TimeSplitters Future Perfect. In TimeSplitters 2, shooting them will eventually set off a small explosion that will harm those close to the explosion, but the crate will not be destroyed. In TS3 they are destructible and available for custom MapMaker Story maps. They can also be picked up with the Temporal Uplink, which can in turn be used to kill enemies when you do not have a weapon.
Crates are usually too small to be used as cover, unless you are playing short characters such as Monkey. The crate cannot completely block a doorway.