Gas Furnace only, is Y wire needed?
You'll want to pull a new cable

The installer who put the existing programmable thermostat in didn't pull the correct kind of cable -- they grabbed a spool of network cable and used that instead.  Problem is, network cables use much thinner gauge wire than thermostat cables (22-24AWG for network cabling, 18AWG for thermostat wire), which means that the voltage drops over the cable become excessive due to the improper substitution, even with the doubled-up wires.

I would suggest pulling an 8-wire, CL2 rated, 18AWG thermostat cable at a minimum -- if you can get 10-wire, 12-wire, or 13-wire stuff, all the better to avoid having to put someone else through this chore again.  The unused wires can simply be wrapped back around the cable jacket at each end.