I find that this can really be a problem on some setups and not so much on others. An acoustic played thru an electric guitar amp accentuates (in my experience) the squeaking. Also, some acoustics, for reasons I don't know, squeak more than others.

My techniques :

1. strum during chord transitions to cover the squeak (as noted above)
2. fully lift the fingers (this is possible, just no fun)
3. use chord shapes that are near each other on the fret board (instead of playing barre chords up and down the neck)

Hope that is useful.

Jon