Mac OS X - software for storing ideas, code snippets, files, etc

"While most of these are not free I highly recommend checking out:

Yojimbo - Designed to store passwords, files, notes, etc. I personally use this for one off notes, passwords, etc.
EagleFiler - Similar in concept to Yojimbo
VoodooPad - A wiki on your desktop, great for storing near everything. That said the free version does not allow embedding files. I personally use this as well and use it for 90% of what you've listed.
Code Collector Pro - Fabulous for code snippets, there used to be a Lite (free) version (you can still find it if you search). I've used the Lite version and it was fine for code samples."

I use Notational Velocity and sync it up with DropBox. It doesn't hold files, but DropBox will easily sync your files on it's own.

DevonThink would do what you want and while it is not free, it was available through Macheist a couple years back, so it appears the developers are open to distributing it inexpensively from time to time. Keep your eyes open.