I plan on starting a playthrough of Fallout 3 soon after I finish Trails Second Chapter and I can't seem to find any reliable/collated lists of mods, so I figured I would try to get it from the horses' mouth.

Boring or not boringness of Fallout 3 aside, what mods would you recommend?

While I can't remember what mods I used when I played F3 for the third time, I do remember a mod called FOOK. Basically, FOOK changed/ added a lot of things in F3 and raised the difficulty too (like OOO did for Oblivion) and I liked it, but I can't guarantee you'll reach the endgame trouble free as I'm not aware if there are any bugs.

Other than that, I remember I used some sort of "Trees" mod, that placed foliage into F3 world, because I couldn't stand it's uglyness after a couple hundreds of hours, but I can't remember how it was called. I can check out though when I get back home, although I'm sure you'll find it on Nexus.

That being said, I should revisit F3 sometime, only to finish the DLC that I left unplayed.

Check out This List. Lots of good stuff there.

I just completed a run with minimal modding, but what I did use is listed in post 1923 of this thread.

Does the Nexus Mod Manager count as the Fallout Mod Manager?

Edit: Oh man this list is good. Some of these mods look to work at fixing some of the issues I had with the game years on years ago.

They do essentially the same thing, so go with one or the other. I used FOMM for my game.

Oh dear, how can I ever decide which ones to use and which ones to ignore in my next playthrough?
So many great mods but I've only got 4gb RAM and will have to refrain from using some of those. :/

The best mod for Fallout 3 is Fallout New Vegas. :P There's a mod for New Vegas that puts the FO3 original campaign and maps into it, with all the engine upgrades and weapons packs from new Vegas.

The biggest must-have for me was moddable weapons and weapon workbenches to improve items, and craft new ones. There was also a mod or two that made some of the useless junk in the wasteland a little more useful, and the ability to craft ammo was fantastic.

I would recommend a mod that makes the history have some sense.
Oh, wait there isn't one.

:P