I was thinking about a few things I've picked up over the years and although they are small things they make a big difference in my playing. At least in my mind. Now in could be some people just did these things from the start by instinct but I admit mine come mainly from watching and listening to others.
Anyhow here's a few to get the ball rolling, please add yours so this thread can become a little fountain of knowledge.
The guitar is never going to be absolutely in tune all over the neck
The best you can do is get it so nothing is really offensive anywhere on the neck. You can sweeten it to the song, slightly flat 3rd for example, make sure the most used chords are sweet tuning wise and use your finger pressure to a certain degree but it's an imperfect instrument and the least offensive is the best anyone can do.
Don't hit all the strings with the same force.
This is very important with riffs and when you are playing bass notes, bits of chord and the lead line. It needs to be thought of as a drum kit and therefore 6 separate instruments grouped together. Balance the volume of the strings with your fingers so parts are louder than others when needed or so the strings that are naturally louder are tamed down a bit. Pick some notes closer to the bridge for less force but more brightness.
Fret as close to the actual fret as possible and pick your harmonics there as well. The intonation of the fretted note will be better and the harmonic will ring out easier.
So, what you got ?