Ahhhh, a subject I've been looking into for sometime. The "ruggedized" watch versions have great value for their price point like G-Shocks and are durable, hence very popular with the troops, so are the Trasers/Luminoxes. There are also those from Chase-Durer (Mike Westen/Burn Notice) and MTM (Jack Bauer/24)
However, for the true, battle-bred MILSPEC watches that are sometimes issued to real-deal operators being paid the big bucks:
1. Marathons are very popular.
http://countycomm.com/Watches.htm
2. Someone already mentioned the Blancpain "Fifty Fathoms" Watch and its esteemed history -
http://blancpain.watchprosite.com/show-forumpost/fi-4/pi-2698241/ti-449461/s-0/
3. The Zodiac Super Sea Wolf was said to be issued (can't confirm though) and was very popular with the US Navy Seals in the 70's. There's even a petition to bring it back -
http://www.thepetitionsite.com/takeaction/222259874
http://www.timezone.com/library/archives/archives0051
4. Currently, I hear the SEAL's privately purchase DOXA's -
http://www.doxawatches.com/sub800ti.htm
5. The watch issued to the elite German GSG-9 troops; the SINN 503EZM.1 -
http://www.broadarrow.net/ezm1.htm
6. Not sure if the Kobold SMG-1 is MILSPEC, but might as well be! Personally it's up against the Sinn in terms of functional simplicity in design -
http://www.watchuwant.com/watches/kobold-smg-1-pvd-gmt-limited-edition-30-pcs
Holy crap! I'm bumping this to add this awesome piece to the above list. The owner and designer is an active SEAL/Specwar guy. I love how "clean" the design is -

Additional info states that he's also a watch guy all his life and has design input and close dealings from both Kobold and Lum-Tec.
Here's the site - http://www.rescowatch.com//
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