There is an RFE somewhere on what we could consider removing on upgrade, but till then:
Run a ls -la, generally the stuff that's symlinked will point to the current versions.
If somethings got 3+ versions I save just the 2 most recent.
When in doubt, error on the side of caution or make a backup before removing.
You can delete those config.##### Not a whole lot of room freed up on it, but I guess you're just trying to tidy up.
If you're cleaning out your /opt/zimbra/.saveconfig/ folder however be a little more careful. Subfolders for old configs is one thing, but I wouldn't suggest removing your current config.save, etc
Do NOT remove the jdk1.5.x_x folder as we're still using it in 5.0.8
Bug 13487 – Upgrade to JDK 1.6 for 5.0.x series, then
Bug 27890 – Downgrade to JDK 1.5.0_15 for 5.0.6 to avoid 3 sun bugs:
Bug ID: 6614100 EXCEPTION_ACCESS_VIOLATION while running Eclipse with 1.6.0_05-ea - fixed
Bug ID: 6546278 Synchronization problem in the pseudo memory barrier code - fixed
Bug ID: 6693490 (se) select throws "File exists" IOException under load (lnx) - still open but fix planned
It also solves this issue:
[SOLVED] Firefox 3 + Zimbra 5 - TLS Interop issue