I have been using Trello to keep my different lists organized: Inbox, Today, This Week, Waiting For, and Done. Then I use labels to determine priority: Important, Not Important, Urgent and Not Urgent.
Todoist is hands down my favorite. It has integration with lots of other software (Gmail, Outlook for Windows, Postbox, Chrome, etc..). Additionally it has convenient quick keys for adding a task to your inbox without having to switch applications. I find their karma system enticing. I have no affiliation with the company, just a huge fan of their work. I was on a Wanderlust kick for a while, but their reliability has been troubling.
I needed something that lets me organize tasks and notes in a tree like manner, like Workflowy, but with proper documents and more text editing functionality, like Evernote, so I built it myself: https://flownote.io
OmniFocus with Airmail and Slack. True, everything Omni is expensive but the sheer impact is has on my life is priceless. I found every other GTD app too limited.
Things by Cultured Code. Mac and iOS only, though. But much cheaper and more simple than Omnifocus.