I usually store my personal javascripts in sub folders under Scripts (see the screenshot below). This way of doing allows me to keep the Script folder clean, light and easy to organize. This is my personal point of view. Now I don’t know what to do with all the other scripts (jquery, MicrosoftAjax, …) and I wonder how other people organize the Script folder. I think I’ll store them in subfolders like jquery folder or General, or …

Can you give me your point of view?
I recommend a tool called Minify, which will combine and minify all your JS files so you only need one
<script src="/min/f=mod1.js,mod2.js,mod3.js" type="text/javascript"></script>tag.You can store your JS files however you want, even outside the web root, and it won’t matter because they’ll simply be referenced in an associative PHP array in the Minify groupsConfig.php file. I’d recommend this specifically for your situation. For example:
Then your script tag would look like:
After Minify comines and minifies your code, it will cache it on your server so subsequent requests will hit the cache file so the PHP won’t need to process. Of course the primary benefit of this tool is that your users only download a single JavaScript file from your server instead of being forced to open several http connections to download multiple files, which is usually a major performance deterrent.
http://code.google.com/p/minify/