Trello board with lists setup like so:

[Inbox][Queue][This Week][Today][Done][Done Apr 2nd]

Text files version controlled in git:

  /notes/ 
  /notes/project1/todo.txt 
  /notes/project2/todo.txt 
  /notes/project3/todo.txt

Since I'm in terminal all day I quickly jot down todos in .txt files as I go. The real management of them is done in Trello.