Are you going with an acoustic, or an electric?

If it's an acoustic you'll want to check the intonation at the 12th fret, because it's next to impossible to fix on an acoustic. You play a harmonic at the 12th fret on each string, and play the note at the 12th fret. These notes should have the same pitch, you will be able to tell if it's really sharp, or flat.

You also have to make sure it feels right, and that the action is set. If it's an older guitar check to see if it looks like any breaks have been fixed, any glue should be visible to an extent. Check the bridge and make sure it's not pulling the top away from the bracing inside. This usually makes the action higher, and the area around the bridge will be raised. If the action seems high at the 12th fret the neck may be bowed.

Most importantly, when you're looking the guitar over, act like you really know what you're doing. Even if you don't act like you know what the guitar is worth. Ask if they can come down on the price a little bit, act like you're not very happy about the first offer.

If it's an electric guitar, check the action, switches, knobs, and make sure you plug it into an amp. Check the intonation with it plugged in the amp too, and run the notes on each string, from the 10th fret as far as you can go up the neck. Listen for any buzzing, and make sure you hear the pitch go up too.

I would tell you to try bending some strings too, but if memory serves you're still in the beginner stages. I hope this helps you, and let us know how it goes.

JD