There's really no way tell which ones will appreciate in value. It's like buying a car, some you think would appreciate don't and some that do make you scratch your head. Maybe some of the precious metals (solid gold or platinum) might appreciate due to the commodity, but it's really a crap shoot.
I bought my Omega because I loved the way it felt and looked, and I see them on the used market for $5-700 more than I paid for it new from an AD in 2007. I didn't think it would increase in value, but the popularity of the "Bond" watch (blue) kind of kept this one under the radar, coupled with the end of the model in '08 or '09, the demand is exceeding the supply on the used market and they are going for a premium.
When I went to get my Rolex, I didn't like the new ceramics due to the width of the lugs, so I knew I had to look on the used market for one. I found a brand new in box (stickers still attached) Z-serial from a collector in Seattle and bought it. I paid more for the watch than it originally went for, but less than a new ceramic sub. It came down to supply/demand. If I go to sell it now, I'll lose some money but I'll still recoup most of what I paid for it.
I recently saw a Rolex GMT Master Pepsi that was BNIB as well with an asking price of $11k. Not sure what the final agreed price was, but it went rather quick due to the Pepsi being a desired model and production ending in '07. I'd venture to guess the price of the watch from the AD was around $5-6k. They reintroduced it last year but only as a white gold model. Not too many are able to fork over $30k for a watch.
One thing I think helps with keeping value up is the price increases that seem to come every year. I paid less thank $2k for my Omega and a new SMP is around $3k now. How much a new Rolex has increased in the past 10 years would make your head spin.
**edit**
If there's one guaranteed "investment" for a watch, I'd suggest setting aside $50-75k, spend the next couple of years searching for a 5513 or 5514 COMEX Submariner, buy watch, and put it in a safety deposit box for about 10 years.