If you're particularly asking about reference material that you take notes about and would like to search and retrieve and produce reports on, Zotero might work

If you're particularly asking about reference material that you take notes about and would like to search and retrieve and produce reports on, Zotero might work for you. I have many years of research notes on it - it's a hyper-bookmarking tool that can keep snapshots of web pages, keep PDFs and other "attachments" within saved articles, lets you tag and organize them along with search capabilities. Outside of that scope, my files reside randomly somewhere in the ~/Documents folder (I use a mac) and I rely on spotlight to find the item I need. It's not super great but is workable often enough. It's not a silly question! edit: I've been trying to find a multi-disk solution and haven't had much success with an easy enough to use tool. I use git-annex for this and it helps to some extent. I've also tried Camlistore, which is promising, but has a long way to go.