In FO3 GOTY, I can select whether or not to have DLC active when I start a new game.

I wonder if I can do something similar to make a mod in that list by default after installing it- since it's a new set of quests in a new location with a different start, it would have to be for starting new games.

No, I don't think so, but you can simply change how the game starts. Then just activate the mod in FOMM. Then again I may be wrong, but I do not think you can do that. Unless perhaps you get a file that says Fallout 3 DLC, and inside it says This is to keep track of what mods are installed. Leave it as is. Like with Oblivion. Perhaps that is what dictates which mods can be selected when you start a new game. I do not have any DLC however, but I do have both expansions for Oblivion. Here is what the file says when you get those DLC.

It is called DLClist and says this

"# This file is used by Oblivion to keep track of your downloaded content.
# Please do not modify this file.

DLCShiveringIsles.esp
Knights.esp"

So if there is something similiar for FO3, maybe you can just add your mod into the list of DLC. But this is just an idea... hope it helps.

Gunmaster95

I have the DLCs, and sure enough, in the \Data folder there is a text file called DLCList.txt, whose contents are this:

Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm

So maybe Gunmaster is right and you can add your mod name to that list and see if it works.

That is awesome news, I will be experimenting with that once I'm home.