I've sorted out most of the bugs I've been coming across, except for one that I can't seem to find information on: The subway tunnels in some areas seem to have incompletely loaded. Instead of the ground and walls that should be there, it is gray as if you toggled off tcl and started walking through walls. Also, there is still trash and raider walls on the ground even though there is no floor. This does not happen in every tunnel, but is most noticeable in the Anacostia Crossing Station.

Here is a list of what I am running:

Fallout3.esmAnchorage.esmThePitt.esmBrokenSteel.esmPointLookout.esmZeta.esmUnofficial Fallout 3 Patch.esmDestruction.esmFallsChurchMetroFix.esmPhalanx-PointLookout-Navmesh.esmCRAFT.esmCALIBR.esmStreetLights.esmFOOK2 - Main.esmFOOK2 - [[censored]] World And Neighbourhood Kit.esmFOOK2 - [DIK] DLC Improvement Kit.esmMart's Mutant Mod.esmAmmo Bench.esmRealistic Interior Lighting.espRealistic Interior Lighting - OA.espRealistic Interior Lighting - BS.espUnofficial Fallout 3 Patch - Operation Anchorage.espUnofficial Fallout 3 Patch - The Pitt.espUnofficial Fallout 3 Patch - Broken Steel.espUnofficial Fallout 3 Patch - Point Lookout.espUnofficial Fallout 3 Patch - Mothership Zeta.espDarNifiedUIF3.espStreetLights - Wasteland.espFellout-pipboylight.espCASM.espPCB.espCRAFT - Activation Perk.espCALIBRxMerchant.espAuto Aim Fix v1.1.espVDSP-01.espUPP - Pack 1.espUPP - Pack 2.espUPP - Original Perks.espUPP - Experience Perks.espUPP  - Quest Perks.espAmmo Bench - Alien Power Cell.espAmmo Bench - Artisan.espAmmo Bench - CRAFT Plugin.espAmmo Bench - CALIBR.espAmmo Bench - Car Mechanic.espBlackWolf Backpack.espBlackWolf Backpack - Vendor Script Replenish.espSniperZooming.espWastelandMastery.espDCInteriors_ComboEdition.espFOOK2 - Main.espFOOK2 - [EVE] Energy Visuals Enhanced.espFOOK2 - [DIK] DLC Improvement Kit.espFOOK2 - Mothership Zeta.espFOOK2 - [DESTRUCTION] Main.espFOOK2 - [DESTRUCTION] Main - Statics.espFOOK2 - [DESTRUCTION] DIK.espFOOK2 - [DESTRUCTION] DIK - Statics.espFOOK2 - [DESTRUCTION] Mothership Zeta.espFOOK2 - [DESTRUCTION] Mothership Zeta - Statics.espTwilight Zone [Utility Tunnel].espSimms' Ammo.espP94-95.espForce Start The Pitt.espSally Fix 2.1.espFOOK2 Nightvision for Fellout.espWeaponModKits.espWeaponModKits - OperationAnchorage.espWeaponModKits - ThePitt.espWeaponModKits - BrokenSteel.espWeaponModKits - PointLookout.espWeaponModKits - Zeta.espWeaponModKits - FOOK.espAlternate Start - Roleplayers.espAS-R CALIBR Patch ONLY.espStealthboy Recon Armor - CRAFT.espEVE.espEVE Operation Anchorage.espZumbs'_Overhauled_Real_Time_Security.espMart's Mutant Mod.espMart's Mutant Mod - DLC Anchorage.espMart's Mutant Mod - DLC The Pitt.espMart's Mutant Mod - DLC Broken Steel.espMart's Mutant Mod - DLC Point Lookout.espMart's Mutant Mod - DLC Zeta.espMart's Mutant Mod - No Corpse Flies.espMart's Mutant Mod - Hunting & Looting.espMart's Mutant Mod - Increased Spawns.espMart's Mutant Mod - Natural Selection.espMart's Mutant Mod - Tougher Traders.espMart's Mutant Mod - Zones Respawn.espMart's Mutant Mod - FOOK2.espMart's Mutant Mod - FOOK2 - DIK.espCombatEnhanced-Package v02.espSkillCheck.espPhalanx-MainFollowerModule.espPhalanx-BrokenSteel-Integration.espPhalanx-PointLookout-Integration.espPhalanx-OPTIONAL-BROKENSTEEL-WeaponRepairLists.espPhalanx-DogmeatEnemyTweaks.espPhalanx-PerksAndStims.espFellout-SOTD.espFellout-Anchorage.espFellout-BrokenSteel.espFellout-PointLookout.espDestruction - CP - Fellout.espBloodImpactFix.espKHWeaponscanner.espHaldurs Improved Workbench Enhanced.espTriage.espMannequin.espVatsLongerDistance.espMegatonBasemant.espTenpennyGhoulsAtPeace.espTinCanCRAFTing.espMerged.espTotal active plugins: 116Total plugins: 121

Any help will be greatly appreciated!

If i'm not mistaken, you need the mesh fix for Destruction, http://www.fallout3nexus.com/downloads/file.php?id=1904

EDIT: You should probably download the hotfix as well.

You're awesome. Thanks.