Folders within folders within folders. Probably by topic, then by date (years), then by theme/event/author, then name each file properly. Only you know your research and what makes most sense for you. It will be personal so play around, but that basic system worked for me.

The mobile phone pictures I'd save all together as a pdf if they are of a single article for example. It's a question of organising your digital copies in the same way you would paper ones.

Www.Mendeley.com -- love this one.

If you use a Mac, the citation manager Bookends. You can link a document to its citation entry, and if you want it to the app will rename your file. Mine are named by author last name and year, or if anonymous, title and year, and I have a folder for each letter of the alphabet. I search in a Bookends to find the one I need and open the doc from there. I find it helpful to put in notes on obscure things, even a transcription on short pieces, so that they're more searchable.

I actually index by frame number (that is, frames nnnn-nnnn are x source, with perhaps a comment on a particular frame of note). If you can set a digital camera to do ongoing sequential numbering (with "series" for different camera sources) you can index them in Microsoft Access or another database program with the whole citation. I'd also convert a copy of groups of images into a PDF if it was a particular report or source that was published. But either way, this allowed me to filter by repository, search for keywords, and so forth.

I'm not totally positive about the format of photos, but I use Calibre to organize my PDF sources and tag with keywords in addition to filling the metadata on publication date, author, etc.

The app allows you, much like iTunes, to import a bunch of files and you have the option of leaving the files where they are in their file structure or Calibre can create one for you with authors as the top folder.

I also create separate libraries for my non-fiction reading and fiction reading.