Is there a DM tool for organizing my thoughts?

[Ferghis]

You need to go to the monster builder and save it locally, I think. I haven't used masterplan since the update, so I can't say for sure. It used to download all the existing monsters, but Wizards' attorneys sent the programmer a nasty note. Without proper legal basis, I might add, but it would take too much to fight that fight.

Disclaimer: as always, don't take legal advice from strangers. Especially those that do not represent you.