What is the purpose of marking the positive terminal of an 50% duty cycle oscillating source?
Depends on where you see it:


It could be a reference for circuit analysis:  the signal generator would have an associated function related to t = 0. Let's say we use a 1 volt peak (2vpp) cosine.  Without knowing which side of the source is +/-, for t = 0 you wouldn't know if you were at +1 volt or -1 volt, and your circuit diagram would be incompletely defined.  In some software programs (e.g. Microcap) they define the AC source signal with a +, exactly for this reason.
If you are using real equipment in the real world, it could designate e.g. which cable was the black one and which was the red one.  
If the function generated isn't completely AC, then it matters: lots of function generators have DC offset capability.


In the end, it's application specific and it depends on whether the circuit is academic or real hardware.  For some applications, it just doesn't matter and people won't fault you.