The question boils down to how can/should microtonal music be notated. "Microtonality" has come to broadly refer to any music that doesn't conform to 12-tone equal temperament. Microtonality includes a variety of just and meantone temperaments as well as equal temperaments with other than 12 pitches.
Allowing one is going to score for a standard musical staff, then there are essentially two necessary elements:
- A set of "accidentals" to indicate the various gradations of a particular pitch. ("Accidental" in this case might be a numerical specification of, say, adjustment in cents.)
- A legend explaining the tuning for each pitch.
The specifics of each of these frequently vary from composer to composer, piece to piece, and temperament to temperament, but the set of symbols linked in Bruce Adams's answer are fairly standard for quarter-tone music and have been adapted to other uses as well.

As a specific example of the two points listed above, here is the "legend" for Ben Johnston's Suite for Microtonal Piano (1978).

The numbers indicate positions in the harmonic series. The arcs denote pairs of (just) perfect fifths.
(SOURCE: Wikipedia > Suite for Microtonal Piano)
For chords, one way to notate them is demonstrated by the Sagittal System (see "Sagittal: A Microtonal Notation System" by George D. Secor and David C. Keenan, also the source for the below image). It shows the "core" relationship between pitches combined with symbols for adjustments to those pitches.

Another option that applies to both single notes and chords is Ben Johnston's specification of cents away from C. The example below comes from Kyle Gann's article "How the 13th Harmonic Saved My Music"
