If I were you I'd poke around to find an index manager that looks at the indexes that exceeds a threshold of fragmentation. Typically there is a much smaller subset of indexes that exceed say a 30% or more of fragmentation.

If you have very large tables who's indexes are severely fragmented then manually address them first then manage the smaller tables second. It may take some custom code to automate this process and may be well worth the effort.

Keep in mind that this is only the tip of the iceberg when it comes down to tuning. It is, however a good place to start.

Kurt