Now, the key in sounding great like jon, is few things.
First of all - rememeber about palm muting (which is obvious)
Also, the power in riffs and sound does not come from a lot of gain. The less gain the better (ofcourse within reason, you don't want to play clean guitars after all :P ) In order to make it sound right, you have to really put your back into riffing - remember that your picking has to be strong, while your hand has to remain loose when you are playing.
Second - the amp. Jon uses Larry Amplification (custom built by a german luthier/amp maker) and sometimes marshall amps, though I belive in studio he uses a mix of everything :D from what I observed, he usually uses Marshall 1960 cabinets, but they may be in his rider because they are very popular and easy to obtain.
Now, why is the amp so important? Because the tube amplifier gives you a totally different response to the pick attack, it's much cleaner and punchier ;)
And finally, you need a good guitar for that - any Gibson will do for example, because they have this thick and reach sound which is just sweet ;D
And most importantly - practice, practice and practice - it can be done, belive me ;) I have learned to play some IE riffs pretty much the way Jon does it, see for yourselves ;)
http://www.youtube.com/watch?v=r555_ODZUFc&feature=channel_video_title
I hope I have been helpfull - in case of any questions email me @ [email]zakknafein@gmail.com[/email]
Cheers
Robbie
P.S.
I forgot - You have to use thick strings for that - the video I posted is recorded on DR 11-54 strings (guitar tuned in D (whole tone lower then standard tuning)