Obviously, one way around this is simply to go for liquid-fuel stoves. They're reliable, generally easy to use, and very hot. The classic, of course, is the MSR WhisperLite ($60; www.msrcorp.com), but there are others. However, while I use liquid-fuel stoves quite a bit, I also like the convenience and the usability of canister-fuel stoves. They offer the added advantage of being extremely light, particularly for short trips. A Snow Peak GigaPower stove ($40; www.snowpeak.com) and fuel canister, sufficient for several meals, weighs a mere ten ounces.
So what to do? Well, at the risk of sounding extremely non-eco-friendly, my advice is this: Don't worry about it. I'd wager you're doing a lot more harm to the environment burning fossil fuel to reach a trailhead than you are throwing out maybe 100 empty fuel canisters. Short of that, of course, Coleman is at least leading the charge with its recyclable Powermax fuel cartridge ($73 with the Xtreme stove; www.coleman.com).