That is one of the ultimate guitar questions and like everything else in music is totally subjective. I've lost myself a dozen times trying to find and figure out what "good tone" is, and what I've found is that its something completely different to every person you meet. What a heavy metal player looks for in tone is something totally different to what a jazz player looks for.
For me, good guitar tone is something that has all the nuances and harmonics of the human voice. A tone that sings back to me like an old female gospel singer does when she's really feeling it. So here's what I think mainly contributes to getting the sound I'm looking for, but you may or may not be looking for a similar sound.
Like AT said, its the player that makes guitar tone, but even more than the player is the players hands and how they the player uses their hands to manipulate their instrument. Primarily they you attack the strings of your guitar with both your fretting and picking hand.
Your tone will change drastically by changing the way you pick the strings, try using thin picks, then try medium and heavy picks, then try just using the flesh of your fingers. You can slap and pull on the strings like a bass player and coax lots of different tones from your guitar. Picking dynamic is also huge in shaping tone. Play as hard as you can, play as soft as you can, play with a medium volume. Alternate dynamic as you play, this will all change the tone of your playing.
Where on the guitar you pick the note also changes the tone dramatically. Here's a trick I learned from an old Dallas blues player named Hash Brown. Play a single note on the guitar fretboard, keep picking the same note up and down the length of the guitar neck and body until you find the position which seems to have the most "bell like" quality to the tone. This is what many guitar players consider the sweet spot since it seems to release more harmonics from the guitar, and its in a different location for each fret. The general rule is that this spot is located between the 12th and 15th fret on the neck for lower positions on the fretboard and near the neck and middle pickup positions of the body for higher positions.
Vibrato is key in shaping the vocal quality of your guitar tone. Just think of any of your favorite single note guitar players and they probably have great vibrato. BB King's vibrato technique of fanning the whole hand seems to me to sound the most vocal and is well-worth studying if you want great tone. Vibrato should be steady and even and when possible in tempo with the music.
Bending notes sounds different than sliding to notes, bends should be accurate and smooth. Sustaining a bend with vibrato is where I find my guitar sounds most "human."
Equipment is the most obvious factor, but the problem here is that there's a lot to choose from, a lot that sounds good and lot that doesn't. Which I think can be a good thing, think about any of your favorite guitar players, they've all been through loads of gear in their careers and probably still aren't entirely convinced they've got the sound they want. A guitar rig doesn't have to be a static thing. I think guitar players should experiment with sound as often as possible, you never know what sounds you can coax out of something until you try.
As far as my taste goes, tube amps are the most important thing in a setup. A loud cranked tube amp IMO produces the best pre-amp, power-amp, and speaker distortion. I personally don't like loads of gain so vintage fender amps are my favorites, I always play them loud and since I started doing this more often I started to notice I liked the way my guitar sounded a lot more. Stomp boxes I like to be as transparent as possible, they should add to the natural tone of the guitar. For guitars, I play mostly fenders. I don't think there's any guitar that sounds better than a good mid-60s strat, but that's just my tastes for what I like to hear. I'm not partial to any type of wood, what I look for in wood is resonance and vibration. When I play an electric acoustically I want to feel a lot of vibration in the body of the guitar when pressed against my body, usually a guitar that sounds good acoustically sounds at least decent when plugged in, depending on pickups.
And that's pretty much it for me and my guitar tone, but you might be looking for something totally different. Recording yourself whenever possible is a great way to tone hunt, since sometime what we think sounds good live sounds awful recorded, and vice versa.
