Road Cycling - When to throw out a tire?

I just went on a wonderful ride in some heavy rain and wind and managed to get a flat at the farthest point from home. It turned out to be a pretty sharp rock that had sliced all the way through the tire leaving maybe a 3mm slice on the inside of the tire (it was on the top of the tire, not the sidewall). Luckily I had a dollar to use as a boot, but I'm wondering how this cut will affect the durability of the tire in the future. These are relatively new (600-800 miles?) Continental Gatorskins and I would hate to have one die before the tread was even starting to wear too much. Could I make an effective but also permanent boot from some shoe sole or something, or is the tire destined to become one for the trainer?

I have a two or three tires with various side wall damage. I hang onto them for my indoor trainer, but don't trust them on the road. If you cant afford to replace the tire; make sure you put it on the rear wheel for safety reasons.

I've never tried it but have heard from some folks that sometimes you can patch a tire with the same thing that is used for patching car tires. May be worth a shot.

I used an empty GU wrapper as a boot and forgot it was there used the tire for well over a 1000 miles without a prob. The GU wrapper is pretty tough so that might have helped.

A catalyst hardened rubber, hard to find in small amounts
Umm.. like the stuff you use to repair conveyor belts or make molds. You should try to spread the hole a bit first as to get a bit in and as it hardens pull out the toothpick or whathave you, smear a bit on the inside.
If it was bad- how about lightweight nylon stitches crosshatched and seal? (for higher pressure and the poss of the tear elongating.)
A nice use for re-tire d is to cut a section and attatch to your downtube as a gravel guard.

Well, examining it closer made it out to be less severe than it looked while repairing it in the rain. I ended up cutting up an old tire (blown sidewall, but the portion I used was fine) and superglueing it under the affected area. It seems to hold up fine, with no apparent oddities in the way it rolls. I'll probably take it out for a short spin tomorrow to see how it holds up.