Ok, I've been playing just over a year, and I want to see if I can upgrade my gear. First things first, I have a Roland Cube 60. Now, I know that 90% of tone comes from the amp, but I'm simply not upgrading that anytime soon. I plan to get a nice big tube amp in the future, but not now. That being said, what other sort of gear should I get to refine my sound outside of a new amp? I have a junk fab metal pedal, but I never use it. I usually just use the Rfier setting on my amp. So what sort of effects do you think I should look into?

Oh, and right now, I'm playing through a custom agile ghost III with emg 81/85.

A decent wah like a RMC5 (wizard wah), or if you don't want to spend that money a dimebag crybaby. Your guitar and amp are really good for metal tones, the build in effects are quite good as well.
First off, Cubes are awesome amps to begin with I wish I would have had one when I was starting out.

It looks like you should have a pretty decent tone to start with, I would recommend an EQ compressor or and EQ pedal, they won't make your tone extremely different but it does give you a better arsenal to play around with