Smart folders, keep it shallow, and Total Finder
I give a lot of credit to apple engineers because they have thought about this like we all have. I used to use things like separate folders for skype downloads, browser downloads, and all kinds of different folders. But I have found that too many folders defeats the purpose and if my structure gets too deep, folders within folders within folders... then things can become just as difficult to find. I think it is best to stay away from creating too many folders.
The finder is a powerful tool and I suggest that you take the time to learn all of its tricks. go into your preferences and view options and do things like add buttons to your finder. and learn about all its capabilities. I do get annoyed with the number of finder windows that can stack up so I minimize ones I want to use again soon then use <

><alt><w>
to close all maximized finder windows instead of going through and closing them one by one.
I have played with a program called total finder. It adds a lot of features to the finder window such as tabs, and show in two separate finder windows together side by side. The program can be a little buggy and i have yet to try see if they have upgraded it for the Mountain Lion OSX.
Using smart folders it really helpful but not perfect. I would love the function that I can create a set of rules which would allow to say look for files with 'x y & z' properties but
exclude any files with 'q or r' properties. It doesn't have a clear way to exclude, that I know of. If you know different symbols for a web search, then you know that they have this capability. If anyone knows how to do this in my smart folders then please tell me.
So I create smart folders and drag them into my sidebar. I tend to follow the default placement of files and let most things reside in my documents folder then use the finder search or the different column headers. Since usually i am concerned with finding things that I recently have been working on. I set my default finder view to 'date last modified' and add to my finder columns the 'date added', ' date last opened', and 'date created' because if a document doesn't show up at the top of a list for 'date last opened' then one of the others usually will get me where I need to go. recently used documents may not show up at the top of o. Plus 'size' 'file type' 'name' are great for sorting through and finding difficult to find files.
Regarding pictures and movies, I like to keep them in my iPhoto library which is now integrated with my Aperture library. It is a really nice way to keep not only images organized, but you can put videos in it as well. Now with OSX10.0 they even have a great feature which allows you to save an image from your internet browser straight into iPhoto.
As for music, I have the preference check which allows iTunes to copy music files and put them into its own file structure. But you better remember to trash the music files after they have been successfully added to your iTunes library, otherwise you might add them twice and create duplicates.
There are many things I could add but the list is long. So all I can say is learn your finder and take the time to learn new features as they become available, especially whenever you upgrade your OS, read over the new changes, it is really worth it.