Hey Curtis,
I'm the kind of guy who does a lot of research before I buy and I just had long talks with Simms about this very matter. The biggest differences (as I understand them) are
1. Gore-tex is more durable and breathes better than the QuadraLam (that being said I've used QuadraLam and it is very good).
2. Headwaters have 13 sizes the Freestone only 7, so if fit is an issue, you might do better with the Headwaters.
3. Headwaters are made in Bozeman, MT, Freestones in an undisclosed location abroad (sweaty and full of 11 year olds smoking knock-off Marlboros)
Both pairs have stitching on the sides of the legs while the Guide series moved the seams to the front and back so they don't rub together (a big deal if you walk in your waders a lot). Also I know some people love the chest zippers (easy on and off), but I don't see any great advantage, because I don't get in and out of the waders a lot.
If you've ever owned Simms waders and sent them in for repair, they should have a report on how you wear out your waders. For me they had 2 such reports so they were able to tell me how I was wearing them out and which model might be best for me in the future. The replaced my $150 Blackfoot waders twice at no charge, and ended giving me (on the second go round 2 years after I bought the Blackfoots) $150 or 40% (whichever was greater) off the price of any waders I wanted. I think they're great. You'll have good waders either way.
This guy loves his freestone:
http://www.youtube.com/watch?v=Dw-NdPS02XkHappy Hunting,
Noah