You know, I think that OOO should be okay to clean. It shouldn't make any changes that are identical to Oblivion.esm. Now I can understand FCOM - it has to make changes to other mods that make changes. But OOO should be nothing but changes. I'm gonna clean it. See if it rids me of my 15 - 30 min CTD's.
I don't believe it's recommended to clean OOO - which has intentional dirty edits.
If you're getting crashes every 15-30 minutes it suggests your system is running out of resources. Use the console to monitor your memory usage and run Oblivion in window mode so you can also monitor system memory usage via Windows.
You should also run Streamline and Oblivion Stutter Remover if you're not already doing so, as these help with performance. If you have a multicore CPU try altering your OSR ini file as follows:
Set bReplaceHeap = 1 (Note: if using Mannimarco Revisited you'll need to set this to 0 just for when you loot Mannimarco's corpse)
Set iHeapAlgorithm = 5.
Set iHeapSize = 1024.