Most spacecraft use one of two time conventions, or more likely, both of these
Universal Time Coordinated / Universal Coordinated Time / Coordinated Universal Time (UTC) - all expressions are used.
GPS Time
The difference between these two is slight, but changes periodically. The difference is currently 16 seconds, as can be seen on this clock.
http://leapsecond.com/java/gpsclock.htm
The reason for the difference is the failure for GPS time to keep track of leap seconds (This is deliberate, to not have to worry about missing seconds). We do have "leap second" adjustments, the previous leap second occured in Sunnyvale on Tuesday, June 30, 2015 at 4:59:60 PM. UTC time was June 30, 2015 at 23:59:60. A leap second is added to UTC in order to synchronize atomic clocks with the Earth's ever slowing rotation.
UTC is an international standard, established for things where a common time metric is needed across the world. Some satellites move through 24 time zones in a very short period of time (non-geostationary), the ISS orbits in about 100 minutes, so it makes sense to have a common anchor point. Typically, navigation systems use GPS time, while other systems use UTC time (also called "Zulu").
One Astronaut has commented : "First off, we live on Greenwich Mean Time (GMT) - which is a time zone roughly halfway between Houston and Moscow, where our two main control centers are located. So when we wake up (at around 7:00 GMT), it is 2 in the morning in Houston and 11 in the morning in Moscow."
Jeff