I wouldn't use the Scripts directory for this purpose, because all default JavaScript files (i.e. jQuery and others) are placed here. I generally use the Content directory for my own JavaScript (also CSS and images) files.
You can structure your files in seperate folders like your views (i.e. ~/Content/js/myviewfolder/somename.js).
If you want to structure your JavaScript code: you can seperate independant code into different files and you can let it process to one file. Or you can group it into an anonymous self executing code blocks, you can then collapse those blocks. Apart from that, I am out of ideas. (Personally, I would go for different files (there are ways if building different JavaScript files into one file.)
