Spy fiction: Like metal gear solid except it involves disguises and sneaking around in plain sight
Covert Action: Cracking codes, wiretapping, driving, and infiltration. All that have to be done within a time limit. Depending on how you do, you can fail, make next mission harder, or make the next mission easier. Missions are randomly generated
http://lparchive.org/Covert-Action/
The Clue!: More of a heist games but it involves spy elements of gathering info, planning, getting helpers, etc.
KGB: You play as a spy for the KGB as you undercover an evil plot. Game has real time so you can missing things, reach dead ends, an only realize it latter.
The Colonel's Bequest: While not a spy game, you do need to snoop around, spy on conversations. Time moves on when you trigger events. You can play through the game stubling through the plot though you don't get a good score.
The Dagger of Amon Ra: Similar to The Colonel's Bequest once you get to the museum. The interesting part of the game is that you need to be actively solving the plot because if you can figure out the murder at the end, you learn nothing. Endings do change base on what you say.
Maupiti Island: You play as a person acting like a detective. Things happen in real time and you can miss events, get attacked, etc.
http://www.dotemu.com/en/download-game/129/maupiti-island