Shenmue was using your real life clock if I remember correctly

trine 2 menu screen reflected the day night cycle according to your computer time and also planetside 2 has day and night cycle

Majora's Mask is probably the best traditional game when it comes to making effective use of a time system. Shenmue and the Harvest Moon series are also notable for having a major emphasis on time management.

I could be wrong but there was talk of Divinity Original Sin having this feature (think this is the one).

Dungeon Keeper 2 can keep tabs on the system time. Play too late into the night, and the adviser will tell you (out of the blue and with no warning): "Your nocturnal presence has prompted the following secret hint: GO TO BED!"

IIRC the original Project Gotham Racing on original XBox used your local time and location to work out the time in the cities you raced in and show the time of day in that city accordingly

Unfortunatly the cheapskates at MS couldn't stretch their budgest to include a simple CMOS battery in teh XBox so you had to set the time and date everytime your plugged the XBox in again for this to work!

I think Anno 2070 has something similar

MMOs tend to have a 24 hours cycle. But also, being MMOs, they usually don't do anything interesting with it.

Pathologic has day and night cycles, and although the time of the day does not affect which people/services are available to you, it has a direct impact on the main plotline. In-game time may not pass as quickly as in most other games, but the passage of time is merciless. Should you fail to complete the quest of the day before midnight, the consequences will be dire.

Doesn't Superbrothers: Sword and Sorcery have that real time thing going on? Not sure, because I've never played it, but I've heard that you have to wait for certain moon phases to complete some stuff and the moon phases are based on moon phases in real life?

I dunno, may be mixing shit up.

Xenoblade Chronicles on the Wii has a 24-hour cycle, although the day/night cycles really only affect two things:

(1) The monsters you see in the wilderness at night are different and tougher than the daytime ones.
(2) Certain characters are only present at certain times of day.

Also, the Elder Scrolls games have day/night cycles that actually affect the games - many people leave the streets and shops shut up at night.

And Minecraft as well - night is when all the monsters come out to play...

I am reminded of Quest for Glory. A very advanced series for its time in this regard.

Project Cars

http://www.wmdportal.com/projects/cars/

The most beautiful Racing Game I saw so far. It is still in development but as backer you get access to the test builds.

Day / night transition video:
https://www.youtube.com/watch?v=TE3A5EtO58s

Related to this, X for Wii U looks like it has a 24 hour cycle from the E3 preview trailer also.