There are two key things to consider:
- How much will you get for your car?
- How much time and effort will it take to find a buyer?
Resale Value
According to KBB, the resale value of an '09 128i Sport w/ 60K miles is $14,132 whether you select automatic or manual. So, at least for Southern California, you shouldn't expect much difference in what you get for the car if you sell it in about five years. Of course, there's always the possibility that you find a buyer who is particularly desperate for a manual and yours is the only one around, but I wouldn't count on it.
Time/Effort To Sell
For almost all cars, manuals will have both lower supply and lower demand (i.e., fewer cars available and fewer buyers looking for them). This means that the chance of a prospective buyer being geographically close to you are smaller if you're trying to sell a manual. So, despite some of the anecdotes of manuals flying off a dealer's lot, it's pretty hard to predict how long it will take you to sell your car. If you live in a less populated area, you will probably have to cast your net wider and wait longer. If you live in a dense urban area with lots of enthusiasts, you may have an easier time.
Of course, if you go the trade-in route, you will almost certainly get less for the car, but you will also not have to work as hard (unless the dealer simply doesn't want your car--which may happen if it's significantly older that five years).