I like many of the options that were proposed however, here is the model I would like to see.
All leftover units, except standard air units (Aka, not VTOL or helicopters) would be converted into Mercenaries. These mercenaries would either:
1. Join another civ and work for them under a contract. of course, they could break this contract if they feel you are being unreasonable. They could join any nation, including ones that they were waging war AGAINST. If they joined an enemy, it would probably require a higher cost. This would include techs that were out of reach for the civ that acquires them. It would require higher maintaince costs "since you dont know how to maintain them." There should also be a permanent agreement where they join the civ permenatly.
2. No one puts them under contract, so they support themselves by looting cities, trade routes, and the such. If they capture a city, they can keep it and either re-start thier original civ, sell it to another civ, or start up their own individual, unique civ.