Almost every musician is likely to be in need of more and better options for portable music storage. Conductors, especially, have trouble with storage of scores, which are often oversized. Give the gift of a conductor's portfolio or art portfolio for safe transport. Meanwhile, directors who deal with large stacks of smaller-sized music may appreciate something like a heavy-duty canvas carrying bag.
A gift certificate to a local music instrument and accessories store is one that's sure to get used by your music director. Musicians of all kinds must visit these retailers regularly to buy supplies like sheet music, manuscript paper, metronomes and equipment for their instruments. Make sure to purchase from an appropriate type of store; music retail is generally either guitar- and pop-music-oriented or classical-oriented.
If you're giving a gift to signify the parting of ways, give a gift of remembrance. If you're part of a graduating class, if your director is leaving her position or if her role as music director was a limited-time engagement (such as music directing for a theatrical production), she'll most likely be happy to have something along the lines of a signed T-shirt or signed group photo, or some other keepsake that will help her remember all of you individually. This is especially good if you have T-shirts made with the name of your musical group or a theatrical production photo. Try your local instrument store for music-related posters, such as a comedic Hoffnung musician cartoon.
Just about everyone enjoys gifts of music CDs but when shopping for a music director, your job is easy. Professional musicians will generally be pleased by a wider array of musical genres and types, so your music director is likely to appreciate it if you try to introduce him to something he's never heard before. Alternately, try to find something new within his preferred area of taste but try to be sneaky in how you find out if he's heard it. Ask casually during chat before or after rehearsal if he's heard of some group or recording if you're considering giving it as a gift.
If your music director has an office with your organization, you can find out if that space needs a little music-related decoration. Figurines, plaques, wall hangings with slogans and posters related to music and musicians can be found at music instrument stores and some mainstream keepsake stores. Many of these are humor-based, so try to find something that you think will appeal to your director's sense of humor.