jab,
I'm going to address certain comments by other posters here just for further clarification.
RE: "
If you want to build tone, gain, feel, etc., put the EQ in front. That's where it very strongly affects the guitaristic aspects of the signal.". This statement not only needs clarification, it needs correction. You can "build" tone by putting an EQ anywhere in the chain, as long as it's before your ears hear it, even after a miked speaker. An EQ can be used for added gain by placing it between the guitar and amp and boosting the overall level slider. This will boost the signal that gets to the amp's pre-amp section, the part of the amp that creates distortion.
"Feel" is an unuseably ambiguous term. As we guitarists typically use that term, it has more to do with how your guitar is set up, i.e., the action, string guage, etc. Perhaps this term is being used as a reference to the amount of sustain that the signal has. If so, then an EQ placed before the amp and used as a level boost will provide more gain, and therefore also more sustain.
RE: "If you want surgical adjustments, as if you were mixing an already recorded track, put the EQ in the effects loop. You can make large adjustments here but probably not in ways that bring out the mojo and naturalness of the guitar.". This is another unuseably vague statement that also happens to be wrong as well. "Mojo"? That's an intentionally unspecific word, and it will mean different things to different players.
"Naturalness of the guitar" is also equally vague, but if it refers to the unaffected signal/tone of the guitar...well, of course that depends on your guitar. Any EQ placed anywhere in the chain can change/affect that tone. No effect will "bring it out" in the sense that the unaffected tone of the guitar simply is what it is. If it's a tone you like, great. If there are things about it you don't like, an EQ can change the amounts of certain frequencies, but it won't change the original timbre of the tone. No box can do that. If you really can't stand that tone, for whatever reason, the only real solution is to use another guitar.
jdurso mentions using an EQ in the loop to fine tune your sound. While the effects loop is where an EQ can have the strongest ability to alter tone, using it to fine tune an already good tone is ideally what you want it for in the first place. An EQ isn't a miracle in a box. It won't make a crappy guitar and amp all of a sudden sound like boutique quality, but it will make a good tone even better.