If you get the following error in the hostname.err log when starting mysqld:
bdb: Ignoring log file: .../log.XXXXXXXXXX: unsupported log version #
it means that the new BDB version doesn't support the old log file format. In this case you have to delete all BDB logs from your database directory (the files with names that have the format log.XXXXXXXXXX) and restart mysqld. We would also recommend you to do a mysqldump --opt of your old BDB tables, delete the old tables, and restore the dump.
If you are not running in auto-commit mode and delete a table that is referenced in another transaction, you may get the following error messages in your MySQL error log:
001119 23:43:56 bdb: Missing log fileid entry 001119 23:43:56 bdb: txn_abort: Log undo failed for LSN: 1 3644744: Invalid
This is not fatal but we don't recommend that you delete tables if you are not in auto-commit mode, until this problem is fixed (the fix is not trivial).