Are multiple wire runs in conduit allowed
Yes, when dealing with single-phase or split-phase power, you can run up to 3 large circuits in a conduit without needing much math.  But aside from all the other amp restrictions, your THHN or THWN-2 wires also cannot exceed this amp restriction: 

Copper:  6AWG-60A.... 4AWG-76A... 3AWG-92A... 2-104A... 1-116A... 1/0-136A... 2/0-156A... 3/0-180A... 4/0-208A...

Aluminum: 4AWG-60A... 3AWG-68A... 2-80A... 1-92A... 1/0-108A... 2/0-120A... 3/0-140A... 4/0-164A... 

Except you are allowed to round up to the next larger available breaker, so #1 Al is allowed for 100A since they do not make 92A breakers.

As long as a split-phase circuit has 3 live conductors, it counts the same as simple 2-conductor circuits.  That's because neutral carries only differential current - any current on the neutral means one of the hots is carrying that much less than its rated current.