I'm making a mod where I want to rebuild 1 or 2 of the forts in Oblivion as a Legion headquarters for Cyrodiil.

Apparently the only legion headquarters in the entire empire is in the Imperial City in the Bastion of the Imperial Prison district.

I figured having some outposts would be cool, but I want to make it lore-friendly.

Alot of the forts in Oblivion already have quests related to them. But were any of them rebuilt in the lore (or were all of them destroyed)? Could one or two be rebuilt while still being lore friendly?

You would be just fine lore-wise if you rebuilt a few of them.

Which ones would be the best to redo?

I'm thinking a couple of the ones kind of further out of the way to support legion foresters and road patrols but still nearish to cities so the legion can man a quick defense if needed.

Fort Nikel, Fort Chalman, consider adding a fort by toadstool hollow, Fort Dirich could be refurbished as some middle of nowhere fort no-one cares about. (For extra fun, make the legion commander there one of the soldiers who torched hackdirt) Fort Virtue, and Fort Irony. These are just some of the ones I could think of that would fit the bill. I reccomend combing over the online map over at the UESP and also checking in-game to see if you can find some forts you really like.

There are a few ruins with no markers at all in the game. I will add to this post after I find them and can give a more specific location, and ensure they are not added by a mod.
EDIT 3-31-2011 The ruins were added by mods. Another factor to take into consideration is location, a Fort in Blackwood or the Jerral Mountains would be a good Fort to send Screwups. Quite a few of the "Forts" were family holdings from the time of Reman, and were abandoned after the Akaviri invasion in the Second Era, but might be used as Mausoleums by the surviving members of the Families that did build the fort.
The legion might occupy and rebuild the upper sections of a Fort, but they would not use the burial crypts.

Ok thanks for all the speedy and informative replies!

I've gone ahead and marked out a few forts that are single or double cell, are near areas where a legion presence is notably absent and is near population areas (kind of dumb not to have any legion there huh?). I also made sure no quests used them or any special loot or NPCs were found in them, just generic monsters/dungeon crawl. There's 4. I haven't decided which ones I want to do or not but I definitely am going to renovate at least 2 (a "legion recruit center" and an outpost near some inns and settlements out in the boonies). I might do another but not sure which of the 2 remaining yet.

Fortunately for me they also don't have undercrofts/mausoleums in them, just abandoned basemants. One of them has a mine area that's been broken into that leads to another ruin. Not sure what to do with that yet. Maybe have some tunneling NPCs or something. Who knows.

My idea is that the Legion has gone ahead and repaired certain existing structures for this politically unstable time (even with the emperor alive Cyrodiilic empire was having issues with the provinces). One fort will be largely intact (I will have to mess with the meshes for the structure quite a bit for this to work out) and the other fort will be just the renovated basemant and then wooden palisades added on top, showing it's a "recent" project.

I have a very small quest line in mind (become legion recruit after fulfilling qualifications, then qualify for special duty [so you can avoid all the arrest duties, patrolling, etc and the scripting problems that would cause] and get sent to both forts for quest updates and get awarded a special "Legion Scout" rank that will let you visit the far flung areas of Cyrodiil and see if any trouble is brewing out there and report back for a small bonus award). I want to leave it open so others can expand on it, or not, to their liking. I just want them there for atmosphere mostly and I don't want any bonuses to be a "must-have" kind of addition so that players can interact with these Legion forts in their own way. IE: like join them, kill them, steal from them, quest for them, or let it be and just look at the pretty additions knowing the empire is 'safer' .

Quests are the easy parts, its the mesh editing I will have issues with as I am very very new to modeling... but my approach will mostly be a copy/paste of vanilla meshes to add floors to the tower and then figure out a simple roof... then use vanilla textures so everything blends seamlessly.

Have you seen http://tesnexus.com/downloads/file.php?id=22965? It adds 4 functioning forts to the game. It uses all vanilla meshes and textures. Thought it might give you some ideas.