Intonation may be relative.
Example: A beginner strumming C7 chords on an out-of-tune guitar will make even a drummer cringe. But take that same beginner, those same C7 chords, that same out-of-tune guitar, and play a Hank Williams tape in the background... well, it doesn't sound so bad now, does it? Context is important.
"Why won't my guitar play in tune?" is a question asked by novices and pros alike. ("What did you do to my guitar?" is another -- I'll have a stab at that one in the Complaints section.) The guitar itself may be fine. It may be surrounded by out-of-tune instruments, thus creating the illusion of your guitar being the offender.
In my opinion, intonation is over-valued, anyway. It's like valuing the timbre of someone's voice over what he's saying. If you're playing something even halfway musical, no one's going to notice that your A string is 3 cents sharp. But if you're still dead set on trying to play in tune anyway, here are a few tips:

• If you're playing with others, have everybody use the same tuner.
This will at least eliminate the possibility that one tuner isn't calibrated the same as another. It won't solve your tuning problems, but it should cut down on petty bickering.

• Don't bend notes unless you absolutely have to.
This is simple:
Bending a note = stretching a string.
Stretching a string = changing its tension.
Changing its tension = knocking it out of tune. It may return to pitch; it may not. Why take the chance?

• Keep spare sets of (new) strings in the freezer. (unrelated to intonation)
This prevents bacterial growth. In the unlikely event that you slice or jab yourself with one of them, you won't have to worry about the wound becoming infected.
It's supposed to extend string life, too, but don't bet the ranch on it.

• Don't put new strings on right before a job.
1.) They take time to settle in, and
2.) you may run into complications and be late for the job.
If you can't play in tune, at least be punctual.

• If you're a religious person, say a prayer or two over the strings.
It's never been known to help, but it shows you're serious.

• Hold the guitar perpendicular to the floor while playing.
For some reason, guitars held horizontally don't stay in tune nearly as well.
I didn't believe this one myself, but I had a special harness made, and sure enough! I never tune anymore.