The Fishers will both come with Bontrager wheelsets, the Superfly having the better of the two. Bontrager is the house brand on Fisher bikes, wheels, cranks, stem, bars, seat and seatpost.
Air9 is Niners geared specific scandium hardtail, while the Jet9 is the short travel FS bike from them. Jeff, the EMD is the aluminum one, as per Niners site.
Paragon comes with Rhythm Comp wheels. Its Bontragers wider profile 29 rim. Its a little heavier, but definitely stronger. Also works well with bigger tires. Bontrager uses formula hubs on this bike.
Superfly comes with RaceXlite wheels. Definitely an xc race wheelset. Essentially it uses the DT 240 hubs with the hubshell built to bontragers specs. If the superfly is in your budget (3000) its definitely a sweet rig. Juicy Ultimate brakes work awesome and are light. Fork is a step up from the paragon (f80 rlc) which gives you a bit more fine tuning. Has carbon cranks too. Don't forget... lifetime warranty.
Niners are awesome too. Unfortunately it would cost a bit more for a similar buildup. If it were me, and I had a ridiculous bonus, I'd probably lean either to pimping out a paragon or building up a niner. I ride hard and crash hard, and that's the only reason I would not consider superfly as a personal bike. Its also cuz like most of us, I can only afford to have one bike.