I have spent all day fighting with Fallout 3. As soon as I started adding mods, it started crashing again. I went through all the 'standard' tweaks: updated my video drivers, reinstalled the game, set it to run as administrator and in compatability mode for Windows XP, ran it in a window, used New Vegas Anti Crash, etc... I even tried a couple of the Windows 10 fix mods, that have you put a d3d.dll file in your base Fallout folder.
What finally seems to have worked is the
Fallout Anniversary Patcher mod. It does a lot of things, the main one being downgrading the game to the previous version (which worked better with mods). It also removes the Games for Windows Lives stuff, makes the executable large address aware, fixes a mod limit bug, and more. It works with both the Gog and Steam versions of the game.
If you are using FOSE, don't start the game with the fose launcher file after installing this (It won't let you if you try). Instead start it with Fallout3.exe, and it will automatically use FOSE if you have it.
So far so good with this. I hope I am not jinxing it by talking about it.