I have a crapload of music in my house (method books and rep for nearly all wind instrument in addition to all of my piano stuff) so this is a very real problem for me.
I use binders with tabs for the majority of my stuff. I'll sort more recent stuff by genre. I've got lots of miscellaneous and several 3" binders full of game music.
It's easy to sort others by composers and time periods. If you sort it chronologically based on the composer's birth year you can get a nice little history reminder in addition to being able to find what you want.
I also keep a lot of stuff I need rarely in filing cabinets and and I have tons of books sorted by instrument on tons of bookshelves around the house.
I like what my grandmother does. Her piano bench opens up, which is where she keeps all her sheet music for all her instruments so it gets cluttered.
She takes the piece and sorts them into different groups like Christmas or favorites or Bach, whatever she knows she has a lot of. The rest that doesn't fit into a category goes into thin binders so the fir comfortably on my stand. The binders are also good when its a kid playing, the plastic protects the music from damage.
- I used to make copies of each page, then keep them loose in manila folders with the initialed names of the composers. This was nice, because I could lay out all four or five sheets of a rag in front of me and not have to turn pages in the middle. But it was easy to get the sheets mixed up, hard to sort through the folders to find pieces, and the individual sheets where sometimes too flimsy for the music desk.
- I recently bought a bunch of three ring binders, dividers, and sheet protectors--both single page and panoramic (two 8.5"x11") sheets. With that, I could pretty much keep everything organized and minimize pageturns. It was much better for organization, but I find that 1) when I open the pages, the sheet protectors I got were a bit too glossy and it can be hard to see the music 2) the music spreads out even more, so if I'm looking at the far right page, I don't have enough of my left hand in peripheral vision to hit jumps well.
- The binders are nice and I'll continue to use them, but I've also been looking for a solution to let me take music on trips. I've borrowed a friend's iPad and put a music reader (forScore) on it as well as lots of music in PDF format. Now the reader is right in front of me, keeping the keyboard and hands in better peripheral view, but the printed page is rather smaller and I'm forced to turn EVERY page (with a tap on the screen). So, to fix that, I could get a Bluetooth pedal system, but before I do that, I want to make sure that other aspects of the reader are working out for me.
I would also highly recommend getting an iPad, especially for things you're getting as PDFs from IMSLP.
If you're like me, there's probably a lot of stuff you download, look over and then don't touch for a good while. Heck, an iPad might save you money in ink and paper in the long run. I still print some stuff, but most of it I just keep cataloged in Dropbox so I can have access to it fairly quickly on my iPad.