Eric,

Options are available to deal with the situation you described.

If you just want to reduce the backup space need, 3rd party tool such as LiteSpeed, Richard mentioned, is great; if you want to do some fix internally, you can create filegroup(s) and move the "duplicate" tables into them, while keeping the mission critical tables in the other filegroup(s) that support the applications. After a full database backup, you can use filegroup backup to back up these critical tables only.

The first method is simple and does not touch database internal. The second option requires work on database architecture and data manipulation, but it will make the database much better.

Good luck.