* Hepatitis A/B and C (A and B were cured early on so name should be livervirus or whatever, C should remain hepatitis until it's eradicated)
* Herpes types 1 and 2 (1 should be renamed to cold sores since almost everyone has it, 2 should remain herpes until it's cured)
* Nonfatal cancers (especially of the skin) need new names to prevent scaring people, especially if they've been largely cured.
* SSH "private key" and "public key" (should have been called "secret" and "share" so that people would know which to keep secret and which to share.. yes I realize they are symmetric)
I could go on, but you get the drift. I think a problem here is that experts in various fields may have exceptional problem solving skills but be terrible at naming things. I've met many programmers with this affliction!