A large part of it comes down to simple math and a bit of research.
For instance if a Trinket procs 1,000 Intellect for 10 seconds and has a 60 second cool down then the value of that proc is:
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[10/(60 + avg time between CD and proc)]* 1,000 * Stat Weight
You would either have to test for how long the ICD is or look it up. Note that at different amounts of Haste you'll have more / less time between the CD being up and it procing (if it's not on use). Then you'll add the value of the static portion of the Trinket which we'll make up and say it's 500 Haste:
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500 * Stat Weight
For a total formula of:
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{[Proc or On Use Duation / (Cool Down + Avg Time btwn CD up and Proc or Use)] * (Proc or On Use Stat Amount * Stat Weight)} + (Static Stat Amount * Stat Weight)
With procs that do damage you have to see what it hits for, average time between charge builds, area of effect / number of targets affected. These can be a little murkier depending on movement, number of targets in a particular fight. That looks more like:
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{[(Average Damage Amount * Number of Targets Affected) / (Cooldown + Avg Time btwn CD up and Proc)] + (Static Stat Amount * Stat Weight)}
Now "Average Damage Amount" and "Number of Targets Affected" can variate and this is one I'm more comfortable leaving to Althor and others to determine it's overall 'Average' value. However anyone can roughly calculate it's value to them with some pencil math or Simcraft.
The more difficult part (imo) is analyzing different talents and abilities that rely on formulas to calculate their damage and often times interact with several other talents and/or abilities. You have to figure out what's additive, multiplicative, etc.
For all of the above you also have to figure how much time spent moving will affect each, average Uptimes on your spells and average times between MBs... you get the idea.
As it looks right now they're keeping things relatively tight with tuning for us and utility choices are the more compelling ones.
Simcraft is easily one of the most important tools though and being able to use that fully is huge. Comparing different gearsets, spell useage / priority, figuring out DPETs, Stat curves and plateaus, etc.
Edit: Fixed