There are no 3ds rules yet so dats could vary in the future. However
http://datomatic.no-intro.org/index.php?page=search&s=64&m=L should net something, their offlinelist option seems to no longer be in operation though so you are left with clrmamepro.
http://www.advanscene.com/ has 3ds apparently but I have not checked it out (click on dats on the left hand side)
Other games
http://www.advanscene.com/ (click on dats on the left hand side)
Does for 3ds, DS, GBA, PSN and PSP.
http://datomatic.no-intro.org/
Does for loads of consoles including old ones.
http://www.tosecdev.org/index.php/downloads
Aims at being near complete for everything that matters.
Similar software. Varies, there was some stuff for the GBA, DS, PSP and such but it was aimed directly at it. It did very well for what it was though and was tied closely to it, you can find various ones
http://filetrip.net/nds-downloads/utilities/rom-managers-renamers/ (though for most it is probably Rominator) and
http://www.advanscene.com/ (rtoolDS and ndscrc). There is nothing special for the 3ds yet from what I have seen though.
More general software is available though.
ClrMAMEpro (
http://mamedev.emulab.it/clrmamepro/ ) is probably the most notable. There are dats everywhere for it and as it is tied closely enough to MAME and MESS you can get some stuff there.
RomCenter (
http://www.romcenter.com/ ) is the main one to go up there with ClrMAMEpro
I am not terribly interested in dredging up the old GBA era stuff right now. Several of the game emulator frontends have fair management options as well (you may have to pay for some, I have never felt compelled to pay for a frontend though). Likewise there are projects like
http://romulus.net63.net/#features
Downloads. Sorry that is now how we roll around here, for the record though I have never seen one that I trust to do anything good like there might be for TV shows.