I am trying to decide between two furnaces and I want some input on how much parts and labor is worth? Is it better to go with the furnace with 5 years parts/1year labor or 10 years parts and labor?

10 year part and labor is available for many brands these days and well worth it. As far as labor goes, every market is different and I have no Idea how difficult the installation is. More times than not the installation is more important than the equipment. Do your homework on the install company. Are they NATE certified? have they done NCI training?etc. Will they still be in business in 10 years?
Are the prices realitively close? Are you going to take advantage of the federal tax credit? HVAC companies for the most part have a lot of overhead if they are worth their salt and they will be considerably more expensive than a company working out of a shed with no benefits and very little training. Nearly 70% of intalls in this country do not perform as they should because of shabby installations and restrictive ductwork design.
Good luck