@Darius: Instead of notepads - all of your notes could be held in one OneNote window/page...
I'm sure you are correct ... and maybe if you were here in the office and you opened a OneNote window/page and demonstrated it I'd say "wow" ... but I'm sort of a creature of habit ... sometimes it's easier just to do things the same way ... just having a script to open all my notepad files is a big step for me LOL
I am not sure if my first post attempt was successful, so here I try again. I want to suggest an alternative approach to some of your problems.
Instead of notepads - all of your notes could be held in one OneNote window/page. Of cause it depends on the size of your notepad files if everything can be shown nicely in one OneNote window/page.
It is a quite nice tool to keep all your notes. You get instantaneous search in all your "notebooks". You can place there screenshots or document "printouts". OneNote will do OCR text recognition and this allows to search for text in all your images that are in the notes! OneNote can also use various types of tags and search only for them.
Tables, diagrams, equations (with computed answers) and other things can added to the notes!
OneNote used to come with some more expensive Office packages. Now there is a free version (OneNote 2013) with the limitation that the notes must be stored on OneDrive and not on your PC. OneNote works quite well with OneDrive. This allows to open the notes from any type of a mobile device or any web browser on other computer that do not have OneNote.
Check the youtube video for a quick introduction: "Microsoft OneNote for Mac Demo". This video is short and most of things also apply to the Windows version.
It may take a bit of time to get used to it, but after this I am sure you will not go back to notepad files :o)