Hi Adam,
I suspect this will be a long answer. 
I bought my “first” guitar from a major guitar store. It was sold to me as new, but being very new at this, when I got it home, I found it was actually modified. It went back and traded for a new one that was in the box. Here is the story on that plus some possibly useful reading for your question here.
What I have learned so far:
- most things are repairable. you will need to decide if you are willing to do so for the price.
- Inspect any guitar that is out on display - even a “new” one.
- check the neck and headstock for cracks and twisting. This may be a major repair if you miss it.
- check the hardware for poor handling: are the tuners dinged or bent. Did someone slip with a screwdriver turning any of the screws. are the strap buttons secure. are the tuner nuts without rounded edges from improper tightening.
- Do the volume and tone knobs work without a lot of noise (plug it into an amp and listen!)
- Does the pickup selector do what you expect
- are the fret edges satisfactory for you (i had a purchase, unseen, with edges that tore my hands up - it went back)
- fret each position on at least strings 1, 4 , and 6. Does anything buzz severely?
That’s pretty much all I can think of. If you are buying used, then remember it may be modified. If you like the sound and feel, then you are really looking for the disastrous to annoying problems that need more attention than the price accounts for.