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Honestly, a lot depends on whether or not you want FLOSS or non-FLOSS, paid on non-paid etc. Not to mention how much actual work you want to put into your system.

I have two, both of which are nominally "free". The first is OneNote that I use for work. It syncs across all my devices and works really well for someone who uses a Windows tablet as I can both write notes with my stylus and draw diagrams. This functionality alone makes it a stand-out awesome system for me as typically in the kinds of meetings I do (with customers) it's usually frowned upon to sit there with a screen in front of you and a keyboard, but if you have a pad flat on the table and can be seen to be writing notes, drawing diagrams etc. it makes a customer feel that I am much more engaged in the conversation. Believe me, I've seen it when my peers are tapping away at their keyboards the customers tend to look to me for input or information because they feel my colleague is not engaged. Some of my colleagues use pen and paper, but I find my method works best for me... I don't run out of ink or paper... though occasionally I do find my battery in my stylus dead. Oh... and even if I lost my tablet I'd still have my notes.

For my personal stuff I used to use Evernote because it was cross-platform. I didn't need handwriting... occasionally need pictures in a note etc. I even paid for premium for a while and I do still have many of my personal notes in it... though I use the free service now.

What I'm migrating to for personal notes is OwnNote which is an app for OwnCloud. This is a FLOSS environment that is free... but to set it up you do need a server that's on the Internet or at least accessible on your local intranet. The down side is a lack of fat client apps... offline sync and the like. It means that you need to be online to write notes. Now, there's an app for Android and one for iOS, but not for Windows or Linux (that I'm aware of, anyway). This means offline usage is pretty much out. Having said that, the API is open enough and I have enough coding skills that I might throw together a fat client at some point, or I might just wait until someone else does it and contribute. It hasn't been a big problem as yet simply because I am typically online wherever I need to take notes for personal consumption.

I host mine on a server at home and I deal with the front-end connectivity by having an OpenVPN network with a Linode fronting it using NGINX. This is overly complex, yes... I also host my own mail server and web site (still!) so this makes my life easier... but you could just as easily front it on a consumer-grade home connection using DynDNS or some other similar service. Of course, the nice thing about this setup is that it also gives me DropBox/OneDrive functionality that's private and owned by me. It's nice to have ALL my documents stored in a "cloud" because I can selectively sync across all my devices, and then I have a script that backs the whole thing up twice a week to S3/Glacier. Yeah, that's also an additional cost but it's cheaper and more convenient to me than a lot of the alternatives. And yes, my S3/Glacier backups are all encrypted :)

Now, all this said, if there was an EASY way for me to have Dropbox-like functionality against an S3 endpoint where *I*/AWS runs the box, I'd be game

Have a look at owncloud.

You can download already made VM images for VMWare, KVM or VirtualBox, or, if you already run Linux and want something lighter than a VM, you can run OwnCloud inside a Docker container.

The combination of ClearOS and ownCloud enables you to build a Secure Hybrid Cloud offering based upon open source file sync and share technology that is as easy to use as Dropbox, but is hosted in your data center, on your servers, using your security policies, etc. Here are some helpful links: ClearOS Link: http://www.clearcenter.com/Software/clearos-professional-overview.html ownCloud Link: https://owncloud.com/products/enterprise Enjoy!

Not sure if it works like Dropbox (have never used DB myself), but worth a look I guess: ownCloud