
From acoustic analysis, to synthesis, to running learnability simulations, Praat may be the single most useful piece of software for the phonetically and phonologically-inclined. It's free and available for download for virtually any platform.
OT-CC is a version of OT introduced in Hidden Generalizations: Phonological Opacity in Optimality Theory, a 2007 monograph by John McCarthy. In OT-CC, candidates are chains of forms that deviate from the input form by zero or more minimal phonological operations, thus resembling (in some respects) the familiar derivations of rule-based phonology. CCamelOT is a Perl implementation of OT-CC written by Michael Becker which allows the analyst to derive inputs by applying an OT-CC grammar to them, as well as to modify constraints and their rankings to produce typological results.
A huge online collection of linguistics papers that cast analyses in Optimality Theory. Many often-cited and important papers are available for download here.