I've moved to MarkDown, and so far, have been filing them away in my company share.
Despite our size, we don't have a wiki that supports markdown. And the Wiki we do have is woefully lacking in organization and content.
I was considering moving my notes into our Centralized Version Control system, where most of our developers go every day, and understand the structure of very well.
This will also ensure that all developers have access to this documentation. With the added benefit of version control and a proper review process for changes.
Sub-Question: What are your note taking habits?