as Joerg pointed out, another thing to watch out for is stretching the string accidentally. If yuo push straight down on the string, just behind the fret, you should get a good note, but if you are pushing slightly toward the next string, you may very well be stretching the string a bit, and affecting the intonation, as well. When you do this on purpose, you are probably playing the blues, or rock and roll, but it is a very common problem I have seen many many guitar and banjo players do - and one which has a sometimes very sublte affect on the over all intonation.