clrmamepro - GUI tool. Has “dir2dat” function that produces a Logiqx datfile. Supports CRC32, MD5 and SHA1 hash types. See these instructions on how to use this while preserving sub-directories and empty files.
SabreTools - Command-line tool. Has “dir2dat” function that can produce a Logiqx datfile, among other formats. Supports CRC32, MD5, SHA1 and SHA256. Its not clear if it has an option to preserve sub-directories or empty files or not.
GameHeader - GUI tool. Supports CRC32, MD5, SHA1 and SHA256. It doesn't preserve sub-directories or empty files. Has its own output format that is supported by DAT-o-MATIC, but nothing else at the moment.
HashMyFiles - GUI tool. Supports CRC32, MD5, SHA1 and SHA256 and others. Produces text/HTML output. Its not clear if it has an option to preserve sub-directories or empty files or not.