I just got done from a half-hour session of some practice and just playing, and my right (picking) hand had some pains in it during the session.
When I was playing spider exercises and things at the beginning, it felt great - no problems. But as I practiced my arpeggios and cross-picking it began to hurt quite a bit. I'm not sure what brought it on, but I need it to stop. any suggestions?
Take a break. Your endurance will build over time, but if you keep playing when it hurts, you could cause damage that will set yourself back.
Ibanez S7320
Peavey 5150 + Mesa 2x12 Rectifier
Maybe you're tensing up your hand too much when playing those techniques. Keep it loose, yet firm enough not to drop the pick.
Where abouts it the pain?

If you are holding the pick correctly, make sure the movement isn't coming from your finger and thumb (as this will cause strain in those fingers!). Similarly, if the motion is coming from the elbow this is also a bad technique to be avoided (you have less control and it will strain your elbow).

Also, you don't want any part of your arm (from your shoulder to your fingertips) to be "locked up" and stiff. This is excess tension and isn't really needed.

It sounds likely that you are creating a motion from your fingers (as this is what some people tend to use to cross strings), this would show up when you play arpeggios and string skipping. The string skipping motion should be from the wrist and elbow (together!) but usually more from the wrist.

Really look at the motion you are using for this, and if it's not that then you just need rest