For academic research, I find https://www.zotero.org/ useful. AGPLv3 license, good integration with web browsers, and good sync. It has tagging and custom notes although I prefer using folders and a separate note taking app.
It's kind of like Gmail for your papers—keyboard shortcuts, fancy Google Docs integrations, auto-downloading etc. He spent a couple of years after finishing his PhD to make his dream reference management tool with a couple of friends.
[0]: I also voiceovered the video on the homepage. A Redditor noted my natural voice is too cartoon-y for the subject matter which I found hilarious, and have since accepted.
Here they suggest that using iAnnotate synced with Google Drive files works like a charm: http://forum.paperpile.com/t/tip-sync-with-goodreader-on-ipa...