[eluser]coolfactor[/eluser]
How many files are you talking? Thousands? Tens of thousands?
I personally organize uploaded files into subfolders. For example, I'll take the first letter of the file (lowercased) and create a folder for it..
Code:
/upload_1/13300.jpg
/upload_a/apples.jpg
/upload_t/Timeless_Visions.jpg
Your upload code just needs to create the upload folder if it doesn't exist. This technique would distribute you files into separate directories.