It's not a bad idea, I'll do events next, so I'll see if this can done simply (with only XML). But what would trigger Tom? What would he do, after all?
In order to trigger Tom Bombadil, it could be a totally random occurance. Maybe if you have a unit entering a Forest tile (this forest tile representing the Old Forest) could randomly create a Tom Bombadil unit?
As for what he'd do ... Well I can think of two things that he did in the book:
1. He resisted the One Ring
2. Drove the Barrow Wights away from the hobbits
#1 is an
extremely great achievement. Perhaps if someone was working on the One Ring wonder, they'd have to start the "building" process from the start if you had Tom as a unit on your side? Or perhaps this could be a "use-only-once" unit that dissappears once you delay the enemy civ's creation of the One Ring?
#2 the unit could be used to fight supernatural units (wights, undead, wraiths, etc.). Thats pretty limiting however, and I don't think it'd be appropriate to have him roaming around outside of the Forest square you discovered him (Tom would never leave the Old Forest!).
I would go with the first option. You wouldn't be able to move Bombadil out of his single Forest tile, so you'd need to protect and wait to use him once an enemy civ begins production of the One Ring (which I suppose you could get notifications about if you possess a Tom Bombadil unit).
If an enemy unit were to enter the same tile that Bombadil is on, I could either see the unit unable to be taken capture (he's a pretty sneaky guy) or to simply dissappear (with a random chance of him reappearing on said Forest tile maybe? Then other civs could get this unit up for grabs).
Now, if that Forest tile that Bombadil is on is cut down, then I think Bombadil should dissappear entirely (He's a spirit of the Forest: what better way to get rid of one then to chop his forest away?).
Just some ideas, might be better off leaving Bombadil out of the mod.