(1) Basset clarinets (or more properly, clarinets with basset extensions to written c (as opposed to basset horns, a different instrument, narrow bore alto clarinets in F with the same written c extension)) are useful. The Mozart Clarinet Concerto was probably written for such an instrument. Should be more of them.
(2) Ophicleides. The rattle made by these brass-winds is more terrifying than a tuba will ever achieve. Essential to the Symphonie Fantastique. (Check out the Norrington recording).
(3) Natural horns. Essential. With the proper handhorn technique, an entire repertoire, from Beethoven's Sonata in F to the Brahms Trio is taken to another timbral universe.
(4) Trumpets in (low) F. The move of orchestral players towards the higher-keyed trumpets (Bb and C, 4' keys, territory previously associated more with the cornet) is another timbral loss. The darkness of the F trumpet is particularly important in Mahler.
(5) Bassoon consorts. A few makers here and there are making smaller-sized instruments, at soprano/alto/tenor pitches, chiefly for children (or others with small hands), but opening up the possibility of full consorts of modern bassoons.
Addendum: Gordon Mumma wrote to add the following:
In your orchestra series, you justly
complement several neglected instruments.
Re the natural horn, it should be extended
earlier than Ludwig's Op. 17. It should be
heard it in J.S.B's Brandenburgs, and later
than the Brahms Trio into Ben Britten's
Serenade for Tenor, Horn & Strings.
Even my old HORNPIPE requires it, etc.