Canister stoves are easier and for philmont most of the issues with them will not be an issue.

If your worried about weight.....msr pocketrocket is a great stove.

Isobutane worked extremely well for us at Philmont 2010.
We will be using it again for our 2012 Expedition. IWTGBTP!

Isobutane Pro's/White Gas Con's
No fuel spillage a) in packs; b) while preparing pump; c) while removing pump; d)while pouring from large bottle to "cooking" bottle; e) if fuel tube comes loose from stove(big fire hazard); f) If pump to bottle connection is worn/leaks/improperly fitted.
No pre-ignition flare from fuel cups to warm the vaporizer tube.
Safer for all the reasons above.
Have to carry White Gas cans' regardless of full or not for the duration of the trip.
Can dispose of the Iso Can's at various Philmont locations.(Must Puncture and crush cans before turn-in)

Isobutane Cons's/White Gas Pro's
More Fuel canisters to worry about.
Have to carry empty canisters(which weigh nearly nothing) until you can dispose of them.
Isobutane isn't as good in the cold (in my experience 20/30 degrees F or less) especially if drawing with the port UP(drawing vapor) ,in some systems can use with the port down(drawing liquid)which avoids the cold+altitude issue MUCH better. In either case, carrying the "next" cooking cans in a Jacket against your body or Sleeping with them in your bag mitigates this issue - it has only once been an issue for us and we took no precautions and still managed to cook with them. This should not be an issue at Philmont unless you are doing a cold weather (Fall/Winter)AND altitude(>10,000ft) trip outside the normal Philmont summer season.

Pocket Rocket is a great stove but the pot, and windscreen must be considered along with the efficiencies/inefficiencies of combining disparate systems - I really like the combination in the Jetboil Helios System http://shop.jetboil.com/index.php/helios.html It did really well for us last year in combination with two Jetboil PCS's(one of which we dual used with a 1.5 liter pot and recommended accessories to convert to one Jetboil to a GCS. I am trying to source 2 Helios's and one Jetboil PCS per Crew for 2012, Our Troop thinks this is the ideal balance of cooking capacity/clean up water availability and weight. We found we used 8 Fuel canisters for 2010 for the 12 day expedition and carried 12 - we will probably carry 12 again next time.
(This message has been edited by Gunny2862)(This message has been edited by Gunny2862)

Keep in mind that regardless of what fuel/stove combination you choose, it is difficult to bring/get the fuel to Philmont. Airlines, trains and busses do not want to transport fuel. So, make sure you can buy what you need at Philmont.

My preference was the isobutane with a JetBoil.

After two successful treks with liquid fuel, I can recommend it. We had no problems with leaks or other problems noted in previous posts (not to say that they are never a problem just that we were careful and had none). Stoves were Coleman Peak 1's and they all functioned great without problems providing a hot meal quickly and reliably. The fuel containers get lighter with time and back country stores stock fuel. Plus, to be environmentally friendly, why use compressed gas canisters that end up in a land fill somewhere rather than reusable fuel bottles? Either way, you will have a great and life changing time!