The SQL Server agent checks whether the job is already running before starting a new iteration. If you have long running job and its schedule comes up, it would be skipped until the next interval.
You can try this for yourself. If you try to start a job that's already running, you will get an error to that effect.
Which version of SQL Server are you using? This seems like a pretty easy thing to test. Set up a job with a WAITFOR in it that inserts a single row into a table and set up the job to run twice in quick succession (shorter than the WAITFOR DELAY).
When running such a test in SQL Server 2005 it skipped the run that was overlapped.