If your talking about breaking 'custom' scripts out of your view and placing them within a separate folder for the purpose of testing your javascript then yes you can place them in a folder of your choice.
However, I wouldn't recommend placing them side by side your view...that's going to lead to a messy project structure and will make it that much harder if you ever want to minimize your javascript.
I generally leave "framework" javascript files within the Scripts folder for the reasons that Mystere Man mentioned in his answer however, I have put 'custom' or view related javascript files within /Content/js/
.
To reference them you would simply add a reference within your view or master page (layout):
<script type="text/javascript" src="@Url.Content("~/Content/js/somelink.js")"></script>