>> Cat5 has 4 wire pairs. The GPS needs 5 conductors.
>> So what would be the best setup for minimal interference and optimal
>> performance? Can the wire pairs be of any use? Or doesn't it really matter?
> 
> Wire it like this:
> 
> Pair 1: Red (+5V) + Black (GND) [the thicker black one]
> Pair 2: White (TX) + Black (GND)
> Pair 3: Green (RX) + Black (GND)
> Pair 4: Yellow (PPS) + Black (GND)

It doesn't really matter at this data rate, but pairing signal with ground is
generally a good idea.

But since the wire you're using is not very thick, I'd use BOTH wires in the
first pair for power (red).  That will reduce the IR drop along the length
of the wire.  That will give you two +5V lines and three GND lines, and
one wire for the other three.
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