Oh, good, here's the thread to report these.
http://www.fallout3nexus.com/downloads/file.php?id=376
http://www.fallout3nexus.com/downloads/file.php?id=13361 (One of the listed compatibility files for Powered Power Armor).
PPA - IMCN.esp (Another listed compatibility file)
http://www.fallout3nexus.com/downloads/file.php?id=13430. Part of the Ambient Temperature package.
http://www.fallout3nexus.com/downloads/file.php?id=15087. Voiced overhaul with quests, new buildings, etc.
http://www.fallout3nexus.com/downloads/file.php?id=8874. Skill/SPECIAL uncapper.
http://www.fallout3nexus.com/downloads/file.php?id=14449. Another quest mod.
http://www.fallout3nexus.com/downloads/file.php?id=5925. Adds a perk for beating "Reign of Grelok" game.
http://www.fallout3nexus.com/downloads/file.php?id=9603. Let's you recruit Cross after BS (I don't even know if this is necessary anymore, but it didn't show up in BOSS).
http://www.fallout3nexus.com/downloads/file.php?id=4180.
http://www.fallout3nexus.com/downloads/file.php?id=2656. Megaton house overhaul.
MMH_Even_More_Storage.esp - config file for MMH
http://www.fallout3nexus.com/downloads/file.php?id=2348
http://fallout3nexus.com/downloads/file.php?id=15003. Adds a flashlight separate from the Pipboy.
Flashlight-LOS.esp
http://www.fallout3nexus.com/downloads/file.php?id=12905
http://www.fallout3nexus.com/downloads/file.php?id=9633. Black Rock Shooter outfit.
http://www.fallout3nexus.com/downloads/file.php?id=14205. Big Town overhaul.
TSC Air Support.esm - Mothership Zeta Crew file that adds Enclave Commander-like functions.
TSC Air Support.esp
Hopefully these aren't already there and I missed them or didn't update.
Edit: Found a couple more:
MZC Addon - MZC-IMCN Patch.esp
MZC Addon - Gear Improv-All in One.esp
MZC Addon-Olympus Armory (forecefield).esp [sic]
All from http://www.fallout3nexus.com/downloads/file.php?id=15369
Edit again:
Noticed that:
Mart's Mutant Mod - Natural Selection.esp
Mart's Mutant Mod - Tougher Traders.esp
Mart's Mutant Mod - Zones Respawn.esp
From MMM don't have a note that they're already included in FWE and don't need to be installed if running both. It might be helpful it add that, since I've been using both for a bit and didn't realize it was unnecessary.