So, I discovered a little miracle the other day. I've gone in heavily for Emacs org-mode, which is about 50% of what I want. It's not terribly visible, and what I really want is something that is heavily web-enabled, but in the meantime it's "good enough." Ever better, there's a good Org Mode to-do manager for Android applications, Orgzly.
But what really makes it worthwhile is Syncthing, a "Personal Dropbox" that syncs up directories and folders just the way dropbox does. Everything is encrypted, and the bandwidth use is actually fairly low once the system is synced up. By running Syncthing on my laptop, my desktop, and my phone (and there is an Android app), I've finally got a set-up that gives me the power to manage my to-do lists with a reasonable front-end, a powerful syntax that I understand, and access from text editors, command lines, graphical UIs, and web-based interfaces.
The reason it's not perfect, in my opinion, is that Org Mode is a sprawling utility that doesn't do a good job of associating bookmarks to to-dos. And let's face it, most of the time when we bookmark something, it's associated with a personal project or task that we want to accomplish, even if it's "Read this later for pleasure." It would be nice if Org-mode had tagging, and we could use the tagging ourselves. That doesn't exist yet, and it would be fun if it did. Using at least limited machine learning to say, "This bookmark is associated with these projects" would be super-awesome.
For now, though, I'm going to have to change my Wiki thing into an org-mode system, and then port my Delicious and Evernote archives to that system. Won't that be fun?