Important note: If you upgrade to MySQL 4.1.1 or higher, you cannot downgrade to a version lower than 4.1.1 any more! That is because, for earlier versions, InnoDB is not aware of multiple tablespaces.

Multiple tablespaces now available for InnoDB. You can store each InnoDB type table and its indexes into a separate .ibd file into a MySQL database directory, into the same directory where the .frm file is stored.

The MySQL query cache now works for InnoDB tables also if autocommit = 0, or the statements are enclosed inside BEGIN ... COMMIT.

Reduced InnoDB memory consumption by a few megabytes if one sets the buffer pool size < 8MB.

You can use raw disk partitions also in Windows.