Almost all of them now a days. Atlas, Kato, FVM, Intermoutain, etc.
To elaborate - all of the above (Micro-Trains too), if the loco is of fairly recent production (say the past 5 years?)
For models that have been run (manufactured, not run on the layout) multiple times, the older runs (more then 5 years ago maybe?) may not be - for example, the original Atlas/Kato SD9 is not drop-in-able, but the current Atlas/China run is.
I'm not aware of drop-in decoders for any current Bachmann diesels, but some come with a decoder (like the NW2) and some have a circuit board that makes it easy to add one (like the H16-44).
Both Digitrax and TCS publish lists that match up models with their decoders.