What are the best ways to organize one's research workflow when using multiple Operating Systems?
Here's what I do, to manage everything between a Mac laptop and a Linux desktop. I usually write code and do heavy lifting on the Linux machine, but when at home or reading / writing documents I use OS X. 


All files of a manageable size are synchronized with BitTorrent Sync. You could also use Dropbox, but that costs money for >2 GB. BTSync is free, unlimited, cross-platform, and peer-to-peer.
If I'm writing code or TeX using TextMate on my Mac, but executing it on Linux, I just run rmate on a document on my Linux machine and the file pops up in TextMate on my Mac. It's wizardry, I tell you. It beats waiting 5-10 seconds for cloud synchronization to catch up.
I use Papers3 for my paper library, which synchronizes with my iPad. All the PDFs are kept in my small, free Dropbox account - the file organization is a bit obtuse so Papers3 is in practice Mac/iOS only. Papers3 does have a Windows app, but not Linux. Mendeley will sync with its Linux and Windows apps, so that might be your best multi-platform option for document storage and annotation.
I have not used Evernote recently, but it runs using Wine in Linux. That's another option for syncing notes and documents.


I'm not aware of a tool for Linux which comes anywhere close to Spotlight for Mac. If there is a program that will synchronize file tags and such across operating systems, I'd like to know about it! Otherwise, for advanced "metadata" and such you're usually restricted to the ecosystem of a particular application.