JMF is, as far as possible, quite outdated, unsupported, difficult to distribute, and in my experience has quite a few unpleasant errors that occur when you least expect them. And if you can make FMJ work at all, good luck - they are proud that it is relevance, slowdown of substitution, but my experience makes me distinguish between these two points.
Personally, I would not even think about it - just use separate libraries for each format or group of formats that you want to support. JLayer will be good, since it can do quite a bit, JFlac will make your flac files on top of this.
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