Oh man, I am a HUGE fan of OneNote...
In addition to text, video, images, urls, content from urls, OneNote also lets you embed audio and any other files you might want, even executables.
It has ink features so you can write long hand if you're using a tablet, then later "lasso" the script and convert it into text using the builtin OCR. You can also draw on a page using your tablet. Pages can be as long and as wide as you want, and will automatically vary in size in concert with what's on the particular page.
Moving things around is easy whether within a page or between books. It creates a sort of textbox of grouped content for dragging around to a difference place. The organizational structure is "books" containing "sections" containing "pages" and you can even have "sub-Pages" if you really want.
You can make your own templates for different kinds of pages (note taking, analysis, experiment, for example) and everything (excluding the embedded files) is instantly full text searchable. Everything you place on any page, including audio files, becomes fully searchable.
The one downside is that it won't, as far as I can tell, incorporate other types of embedded files into its search index. Sure it will make the file's metadata (like name) available within search, but not the file's contents.