Conveniently BECMI, which is always my system of first choice, has a random dungeon stocker, modified from the original Holmes.
Wilderness stockers have been discussed both here and here. Paolo and Brendan have perfectly workable systems which I like, but I would tweak things slightly. My position on hexes is something I have made clear in the past so there is no need to belabour the point, but assuming a default of 6-mile hexes, each hex should have at least one pre-rolled adventure site, not taking into consideration random encounter-based results that flesh out the map further in-game.
That said, I want there to be a distinct difference between Faerie and the "real world". Faerie is supposed to be where adventure happens; the "real world" is more mundane. I also want New Troy to be small, at least at first. Initially, the map is going to be 1-mile hexes. A final consideration is that I want New Troy to be overlaid by the map of Faerie: Faerie is a kind of mirror or reflection of New Troy, with a certain special twist.
So the idea for stocking the New Troy map is as follows. First, I place the starting settlement plus a few others. Then, I stock the map with something like this table, rolling for each hex:
1. Opening to Faerie (tied to a certain natural landmark; may be known or unknown, permanent or temporary)
2. Beast lair (wolves, bear, boar, etc.)
3. Human mundane (thieves, knightly manor, village, etc.)
4. Human special (witch, monastery, hermit, etc.)
6. Hidden or special place (crypt, cave, hollow tree, standing stones, etc.)
Once this is done, I overlay the New Troy map with the Faerie map, and flip it so that each hex in Faerie corresponds with the New Troy ones as follows:
1. Opening to Faerie -> Opening to New Troy
2. Beast lair -> Monster lair
3. Human mundane -> Faerie ('Mundane' seems the wrong adjective)
4. Human special -> Faerie special
5. Ruin -> Magical location (wizard tower, magical lake, toadstool circle, etc.)
6. Hidden place -> Transplant (a building, person or thing that has 'slipped' from New Troy into Faerie)
Then I decide where the opening(s) to Muspel are. I haven't tested this, so it may result in skewed results; we'll see.