I'm searching for an app like iTunes or iPhoto but for documents which manage documents for me.
I assume the finder itself could manage documents, but please explain how the helpful properties of finder or another app can work more like iTunes and iPhoto on OS X.
The closest analog I know of for general purpose document organizing in an "everything box" similar to iPhoto/iTunes would be Yojimbo.
It lets you catalog and organize information in quite powerful ways. Also check out Evernote if you want files to be in the cloud and don't already use a service for syncing. I've heard Together is also worth investigating but never really known anyone that used it or tried it myself.
Finder is capable of using tags and smart searches, but most people that are inclined to do that have already come up with a folder hierarchy that uses the filesystem for storage and spotlight for indexing files. It really depends on how much time you want to invest in cataloging and the volume and type of files you are organizing.
If you're managing a lot of PDFs, I like Papers. It's intended for researchers to manage research papers. I've found it handy for managing other sorts of documents. It lets you specify plenty of metadata, organize documents into collections, and take notes about your documents.
It also sounds like you could use a great primer on using the Finder. Macworld has a bunch of articles to help you learn more about using the Finder, including Finder 101 (which is super-basic) and Mac essentials: files, the Finder, and search (which introduces you to ideas like Smart Folders and lots of things -- it's a long article, but worth the time investment). Macworld has lots of other resources. Your question is pretty broad; if you update, I might be able to provide some more specific recommendations.
