I suggest you take a look at the following:
- the ususal nlp libraries like Open NLP, LingPipe, NLTK, Gate, UIMA. All of these provide parsers and word stemmers (i.e. they don't give you back the root of a word, but its stem). Some also provide lemmatizers.
- websites which collect NLP tools. These are but a few of them: the wiki of the Association of Computational Linguistics, Language Technology World, the website of the compling dep. at Heidelberg University
I'm not aware of a tool which returns the root of a word, but, as I said, there are stemmers and lemmatizers. For lemmatization, try Tree Tagger or Morpha. Morphophonemic analysis is a term not specific enough to get you what you want.
Once you know more specifically what you need, you could search the archives of the Corpora List or post a question there.