The string quartets of Mozart, Beethoven, Schubert, Bartók and Shostakovich are quite often performed and recorded so we can't call them neglected, but the string quartets of Haydn, who not only originated the form, but left us eighty-eight wonderful examples, are not performed quite as much as one would like. Haydn is always the slightly overlooked composer. This is the String Quartet op. 20 no. 2 in C major played by the Quatuor Mosaïques on original instruments:
The music of Bach is widely appreciated, of course, but there are some areas that are neglected and the main one, I think, is the huge repertoire of cantatas for small orchestral group with choir and vocal soloists. These are absolutely unsurpassed examples of religious chamber music that are probably not heard very often due to the fact that they are no longer a part of the religious service they were originally written for. Plus, they require very good musicians and sometimes require some unusual instruments. In addition, we don't seem to have too many appropriate venues for them these days. This is certainly an under-appreciated repertoire for most listeners. This is the Cantata BWV 113 "Herr Jesu Christ, du höchstes Gut" performed by John Eliot Gardiner conducting the Monteverdi Choir and the English Baroque Soloists (further credits at YouTube):
One of the largest under-appreciated repertoires is the five hundred and fifty-five sonatas for harpsichord composed by Domenico Scarlatti and barely known before the 20th century. The only complete recording is by Scott Ross and it is well worth becoming familiar with. Here are fourteen sonatas from the middle: K. 204a to K. 216:
An older repertoire and one that has yet to be really discovered is the music for vihuela by Luis Milan some of which is played by guitarists. Here are some samples. The first is the Fantasia XI de consonancias y redobles with Ernesto Quezada, vihuela (doing some very nice ornaments).
Next Robert Barto playing Fantasías XIII and X:
Finally, Fantasías X and XII played by Ralph Maier:
I'm sure my readers have their own favorite neglected repertoires, so why don't you tell us about them in the comments?