This is a pretty general question, but I will do my best:-). There are several differences between both these stoves, most noticeably the stove itself. The Jetboil's stove is nothing more than a traditional small canister stove. It is very similar to the Alpine Lite Stove made by Primus. The mere fact that it uses a heat sink on the pot and has incorporated this stove into a system makes it different than other canister stoves. However, it is not 100% wind resistant (needs both primary and secondary air), and it doesn't have anything to regulate the pressure being generated by the canster (meaning it's performance is completely dependent on the weather and amount of fuel in the cansiter). The Jetboil isn't very light either when compared to other sit-on-top canister stoves (weighs in at about 15 oz.). I would recommend the Jetboil for those who want a fairly small, compact stove/pot system who primarily boil water. It does so fairly efficiently and quickly when compared to other stand-alone canister stoves. The Reactor is entirely different. The only similarity between the Jetboil is that it uses a heat sink on the pot and is also a stove/pot system (meaning no other pot will work on the Reactor other than the included pot). The Reactor's stove is truly innovative in that it uses a pressure regulator (meaning it only needs about 12 psi to obtain optimum heat output compared to 65 psi for every other canister stove including Jetboil). It also needs just primary air (primary air, located below the stove's burner head, is where 60% of the stoves combustion is generated...secondary air, located between the stove's burner head and the bottom of the pot, is where 40% of the stove's combustion occurs...block either of these off and the flame will go out). The Reactor's need for only primary air makes it 100% windproof by allowing the pot to rest directly on the burner head thus protecting the heat output. The Reactor is the only stove that will give you consistent 3 to 3:30 minute boil times per liter in any condition above about 10 degrees. The pot is one of the most innovative pots for heat distribution and efficiency based on its laser-welded heatsink and 'shroud' (the shroud captures any heated air and traps it for a moment to help improve efficiency...the holes around the circumference of the pot allows this hot air to escape-it's also laser-welded on). Just to be clear, the pot has been updated and is now lighter (about 10oz.). The stove weighs in at about 6.5oz. making the complete unit (without fuel) weigh in at about 16.5 oz. If your interested in sheer performance and efficiency, the Reactor is the stove. If you want a smaller stove system and are willing to give up some performance and efficiency, and plan to only use it for solo use, the Jetboil might be the better option. Remember, the Reactor can boil a liter at a time whereas the Jetboil can only boil 2 cups. Hope this helps....