Cheyenne ArcServe has a Notes agent which lets it back up open databases. The agent requires a "work area" of the size of your largest Notes database because it creates a replica of a database into a separate directory before backing up that database.
Tivoli TSM (formerly IBM's ADSM) will back up open files and can back up databases incrementally.
Veritas's Backup Exec with the Open File Option (they also have a Domino agent).
Quadratec's Time Navigator can do full and incremental backups
Unix's tar (and ports of it to other platforms like NT and OS/2) will back up open files.