Heavy Evernote paid subscription user here. Why paid? because it indexes images, pdfs, images inside pdf's etc. It has easy integration with a lot of other tools and services, doesn't have a Linux client (for which i blame them) but still i consider it my best option so far.
As much as i like evernote over all the other solutions i found so far, it's still far from perfect. Especially the UI and lack of complex search can be a pain. Sometimes it feels like an interconnected and smart notepad++ that simply refuses to take the leap... But hey, combined with the other stuff and the API's nowadays, we just hack our own solutions right?
Complete projects go into dropbox because of the file sync obviously and the use of jetbrains tools for code. (pycharm with markdown support and "live" PlantUML is really nice)
A private Rhodecode server holds a lot of code in both git and mercurial. I check out my repo's in a dropbox (linked) folder so i can continue where i left of, and have an automatic backup.
Project related documentation is in the sourcecode, or on a self-hosted Taiga server. Communication about that, and some snippets move through Flock.
And my latest weapon of mass creation is a Wacom Bamboo Slate. Because i still ended up with a lot of paper notebooks everywhere. Mostly because hand written notes and schema's are just so darn quick compared to everything digital. But i ended up with 20 notebooks and the management of those physical things was getting tedious. Also, that stack of paper notebooks is quite heavy. So i'm trying the slate now, which holds a paper notebook but automagically produces an electronic version. Of course it's synced with my phone and from there i can export to evernote. It has tags support, like writing #tag on paper, so i'm working to see if i can get those to evernote.
Hope this helps.