Check all microphone and instrument cables and repair or replace any that are defective. Worn cables and their connections may work intermittently or add noise to the signal chain. Errant clicks, pops and buzzes that occur during a recording can ruin an otherwise perfect take, so get into the habit of checking cables regularly.
Tune all instruments before recording begins. If all guitars, basses and keyboards are not in tune with each other, the quality of your recorded tracks will suffer no matter how polished the performances are. Old strings also will result in compromised audio quality, so change them as soon as their tone begins to dull. If you are recording drums, make sure that the drummer replaces dull-sounding drum heads and then tunes the entire kit. When instruments sound good acoustically, getting quality tracks is so much easier.
Experiment with microphone choice and placement. When you are anxious to capture a musical performance, it can be tempting to just aim any old microphone toward your instrument and then reach for the "Record" button. While this can sometimes help you capture a spontaneous performance, it can often lead to a track of compromised audio quality. Different microphones have their own tonal character and even slight variations in their placement can yield wildly different results. Taking the time to audition different microphone set-ups while tracking will ensure that you get the best-sounding track possible for each instrument.
Record your tracks without special effects. Recording with reverb, delay or compression might seem like a good idea, especially if it sounds better to you in the headphones as you are playing or singing, but once the effects are recorded with the track you are stuck with them. Recording signals dry--without effects--will give you the ability to add such effects to taste at the mixdown stage. If you really like the sound of effects and feel like it helps you perform better, send a processed signal with effects to the headphones while recording the dry one.
Double check the input levels of your tracks before hitting the "Record" button. An otherwise perfect take can be ruined if the signal clips. This happens whenever the signal level peaks above 0dB and all digital information above 0dB is literally lost. Unlike the warm analog distortion associated with vintage tape equipment, today's digital distortion is harsh and unpleasant, so monitor the level meters carefully and make sure that they never go into the red.
Clean up your recorded tracks before you begin mixing. During pauses between instrumental phrases, there can often be errant clicks, buzzes and general background noise, and listening to your tracks in isolation will make these very apparent. Pay particular attention to the beginning and the tail end of tracks, where they will be most audible. If you use the "Erase" function as you encounter them, you will have a cleaner, less-cluttered mix as a result.