It's been answered a few times already, but here we go...
* .ea/.eal: End Actions (The 'Before you go..' popup at the end of a book).
* .mpb/.mpb1/.tan/.tas/.tal/.mbs/.han: Notes, Bookmarks & Progress
* .phl: Popular Highlights
* .azw: Mobi book
* .tpz/.azw1: Topaz book
* .pobi: Periodical
* .azw2: Kindlet (Active content)
* .azw3: KF8 book
* .azw4: Print-Replica book
* .apnx: Page Numbers
* There's also a bunch of other misc stuff in the sidecar (.sdr) folder on the K5: .azw3f, .azw3r, and .asc for X-Ray (among other things).
The .fusehidden files are... let's say ghost files of stuff that has been deleted while it was still in use, to keep it simple. Should never happen under normal circumstances... (Wild guess: Is this a K4, has it been jailbroken but not rebooted straight away after the JB at one point? And/or: do you make it a habit of unplugging your device without ejecting it first?).
The DONT_HALT_ON_REPAIR is a flag file used by the framework to, well, don't halt (shutdown) on repair (the 'Your Kindle Needs Repair' screen). It's always there on the K4 for some reason.
To resume: everything has a particular use. Don't delete stuff for the fun of it (or even to free space up: most of those sidecar files are pretty light). If you find your documents folder messy, use Calibre with a proper target folder template (or, sideload into subfolders yourself. The only time you don't really have a choice is when the device loads content itself [send to Kindle, on-device buying, on-device Archive/Cloud]).
Last edited by NiLuJe; 10-18-2012 at 10:09 PM.