Tuning your guitar is the most crucial part of a quality recording. No matter how confident you are with your instrument, re-tune in between recording takes. Temperature changes in the room, as well as continued playing, can affect the guitar's tuning. Tuning your guitar before each take will save you the headache of discovering an off-key note after you hit the playback button.
As in real estate, location is important to recording an acoustic guitar. Different rooms will make your guitar sound different due to the room's furniture (or lack thereof), flooring and other sound-absorption factors. The acoustics of a tiled bathroom often sound great, but it’s a good idea to do a sample recording in each room to determine which sounds best. Take note of any outside noise sources, such as windows, air conditioning vents and fans: the microphone may pick up these sounds while recording.
Never place the microphone directly over the sound hole: this will result in poor-quality sound, and will pick up the clicking of the pick against the strings. Most professional recording studios place the microphone several inches away from the 12th fret, although this can vary slightly depending on the length of the neck. If you have multiple microphones, try placing one microphone at the 12th fret, then experiment with placing the other at different angles behind the guitar's bridge. Try also placing both microphones at the 12th fret.
Whether you use a microphone to record your acoustic guitar or plug it into an acoustic pickup, experiment with different effects like sustain, compression, reverb and EQ. Record the guitar at its most natural-sounding, then experiment with adding effects during the mixing process. Recording with preset effects makes it difficult to remove them if you later decide you prefer a natural guitar sound.