The problem with having files all jumbled up and relying on searches is that it you have to remember what something is called -- or that it even exists -- to search for it. For me, filing by subject matter works best -- and it doesn't matter what the extension is. I treat files just like I would paper in file cabinets, where there are drawers that contain certain subjects, in the drawers are expandable folders that contain projects, and in those are file folders for individual items.
For example, since I lecture a lot, I have a folder called "lectures." In that are dozens of events, such as "family court judges 7/28/07." In that folder will be a folder for correspondence connected to the lecture, one for the bio I used, etc. I may have a subfolder for materials that contains several files, each containing a separate handout. The extension doesn't matter at all. I may have Word documents, power point presentations, excel spreadsheets, etc. I don't worry about the extension, and only concern myself with organizing everything according to project.
There is a lot more to it. For example, I may copy the bio to a folder called "bios," so I have them all in one place. The same with materials. Within the folder for lectures, I may have a folder called "materials," in which I have copied all the materials I have used for every lecture.
Doing this allows me to get a visual picture. So, opening the "lectures" folder lets me view at a glance all the lectures I have given. I can then dig into any one to see if there is something I can use for the next one, etc.
It also allows everything to be clean. When I open to the first level, I only see 30 or so large project folders, such as "lectures," "real estate," "personal," "financial," "writing," "health and fitness," etc. Each of those contains folders and sub folders, going ever deeper, but still visually simple. Works for me.
BTW, even though software programs have their own preference for default directory, etc., can't you just change that so all of them are downloaded into your program directory? I don't allow a program to put itself anywhere I don't want it.