bitcoind listaccounts currently shows five accounts, only one of which is being used. What's the command to delete empty accounts, or at least remove them from my wallet?

Yes, not implemented yet.  Do you want to remove them just so the listaccounts output isn't messy, or is the lack of a deleteaccount API call preventing you from doing something you need to do?

Also, if they still can't be removed yet, can they be renamed?

I believe a relatively easy solution would be allowing to delete an address, but not deleting its key (so that it becomes identical to a change address).

For the truly OCD people there are two choices that are much simpler than modifying the bitcoin client:

1) write a C/C++ wallet cleaner utility using the matching Berkeley_DB libraries
2) do db_backup/clean/db_restore using Berkeley_DB utilities. The backup format is textual and the wallet database structure is very simple, so the "clean" step can be written in any of the widely known text processing languages like awk or Perl.

Remember that when using Berkeley_DB utilities you may need to create an appropriate DB_CONFIG file to be really on the safe side. This was discussed before on this forum.

In my opinion there is no need to delete empty accounts.