Monitor unusable indexes on oracle
You can use both, Nagios and Oracle Cloud Control 12c (also applies for Grid Control 10g and 11g).

I used Nagios about 8 years ago to run custom SQLs but I guess there is much changed since then. Maybe someone else has recent experiences with that.

In Oracle Cloud Control you have 2 options:


Write your own Agent Plugin. I never did that because after some testing I considered it to be to much work.
Use "Metric Extensions" available with "Diagnostic Pack".