if your guitar has a neck pickup with adjustable tone, turn the tone all the way down in the neck position and, as mentioned above, tune to the 12th fret harmonics.
if not, turn the tone knob down about 3/4 way on the bridge pickup, and roll the volume back about 1/4... and tune to 12th fret harmonics. or, you can leave your tone knob up all the way, tune to 5th fret harmonics on the bridge with active pickups..for some reason, guitars i've played with actives like that 5th fret harm and track well in just about any tuner.
on les pauls, i've found in the middle position with both pickups combined, rolling back on the tone knobs and a hair on each volume (depending on pickup height) for both PUPs and using 12th frets will get you pretty dead on.
with ibanez type, the tone knob tricks above combined with volume (you'll need to find your sweet spots for each guitar basically) works well.
another trick i've used is to put the tuner AFTER the distortion box in the pedal chain, if you can do so without routing your signal THROUGH the tuner, by all means, try it with the above mentioned volume and tone tricks.
hollowbody guitars and acoustics on stage are a whole nother deal...but can be dealt with in a neat way too....
wire an old pickup to an old, unused 1/4 cord thats at least 6 feet long. + wire from the PUP to + / neg-neg. respectively
now, hold the pickup (plugged into the tuner) over the strings and tune.
if you're not using your effects loop from your amp, you can take your tuner out of the pedal chain, use the effects send, and send some signal to the tuner and just let it sit on top of or beside your amp...or run it all the way back out to the pedal board.
