IMO applied mathematics is underrepresented across disciplines.
Ergodic theory usually has several papers in Annals and Inventiones each year, and is regularly mentioned when the work of recent Fields medalists is described (e.g. Avila, Lindenstrauss, Mirzakhani) but I think that there are no more than ten ergodic theorists who contribute regularly to MathOverflow.
Here is a nice statistic: since MathOverflow opened, there have been as many Fields Medals awarded to researchers active in ergodic theory as there have been bronze tag badges issued for answering ergodic theory questions on MathOverflow. Based on current rates of progress, the first silver tag badge for ergodic theory will be awarded to Anthony Quas at some point in the spring of 2022.
With Keith Kearnes participating on MathOverflow (and hopefully asking questions soon), I am confident that Universal Algebra will be represented to my satisfaction. Taking that personal perspective as a benchmark, I turn to the Tags page and note that the universal-algebra tag has been used 20 times this year for questions. I suggest that any tag that a) represents a sizeable area of mathematics, and b) has fewer than 20 questions asked this year is a good candidate for an underrepresented area. In particular, conformal-geometry, mathematical-writing, and combinatorial-game-theory are underrepresented by this measure. I know I would like to see more questions in the last two areas.
Gerhard "And More Pictures From Joseph" Paseman, 2015.08.31
I would like to see more questions in free-probability, whose tag has 13 questions, or more generally in non-commutative probability. While this may be a relatively small area of mathematics it should interest many parties, namely, probability, combinatorics, and functional analysis.