Together with Raphael Finkel (Dept. of Computer Science, University of Kentucky), I have helped develop Kratylos, a program that lets you display, query and browse interlinear glossed text as well as time aligned transcriptions from a variety of formats online. Read about it here and try it out here!
More recently, we have produced an implemented theory of derivational phonology and morphology: the Phonomaton.
The Phonomaton calculates derivations using an extension of SPE phonological rules with a full (modifiable) feature set. It allows for underspecification and can handle autosegmental tonology, among many other things.
The Phonomaton’s cousin, the Optimaton, implements a version of classic Optimality Theory using the same feature set and similar notation. See the library of examples to get a feel for the syntax, which should already be mostly familiar to phonologists.
Finally, the Morphoton implements a theory of morphology similar to that proposed in Anderson’s (1992) A-morphous Morphology and is built on top of the Phonomaton with all of its goodies.