It's all about databases, and many things have become a database at this point. We expect to search data quickly, thanks to google and gmail. Services like Dropbox are sort of an exception, with their nested folders, but even Dropbox has introduced searching to some degree. The other important apps, such as Evernote, Devonthink, email, and Spotlight (heck, even the internet itself, except for the deep weep and dark internet) are all deeply rooted in search capabilities.
It gets tricky, as the more complex and comprehensive the database the harder it is to find things. That was my frustration with Evernote a year ago or so; I started putting everything in it, and it became too hard to find things. The other option is to have multiple databases, which causes fracturing and forgetfulness (where did I put that?), but does keep things clearer in terms of storage and searching.
I'm currently playing with Ember. It's a beautiful app, and spiffy in terms of sync and usability. For pictures you want to use for blogs and presentations, it really shines, and is much better than just relying on the photos app where things get buried with your personal stuff.
Evernote is great for archiving purposes. I love it for operating manuals and such (just the other day, I had to change the settings on the stereo receiver at home – with Evernote, I had the manual pulled up quickly and easily). The presentation mode is really interesting, and I'm looking forward to playing around more with it. It could replace PowerPoint in many ways, and would unify work, search, research, and presentation.
I really like DEVONthink for my work. It provides a clear and easy workspace for various things, and is really powerful at search and filing along with being a great native Mac app. It is rock solid, never crashing or causing problems. It's the sort of place you can work and reuse research, notes, and various materials. You can use images in DEVONthink fairly easily, but it's fun to use Ember instead.
nvALT is terrific for those little notes and references points, so that they don't stay in your inbox, head, or misfiled. I use Simplenote on the mobile devices to sync with nvALT (or is it vice-versa? I forget).
Dropbox is great for storing and accessing files, and sharing them as well. My co-editor and I edited our book using Dropbox. iCloud also works well for universal access and storage, and Google Docs and Drive are also great for storage, sharing, and collaboration.
We mustn't forget about good old email. It seems old-fashioned and stodgy, but it is still a workhorse and the easiest way to communicate clearly with others. You can search it for old emails, attachments, and information. While the inbox is annoying and interruptive, we are more to blame than email (we check it too often, and we use it as a task manager).
So it's all a bit of a mess. Perhaps living and breathing in one database alone is best – one ring to rule them all. You would know where it is, and not go searching various places. There would be no new learning curves or applications to try (though where's the fun in that?). Yet you would also suffer from size, difficult searches, and lock-in. With multiple databases for multiple purposes (sort of following the mobile computing app model of using different applications for different purposes), each database is separate, clear, and functional.
At least for now.