I am constantly fidgeting with my productivity apps and system. I was engaged to Paperless for many months, but now I am playing with Todo.txt on the command line and on iOS. As a result, I've been thinking about types of lists and the most appropriate apps for each type of list.
These lists include only tasks that require a physical (measurable/observable) action to mark as complete. This is what the GTD system is all about. Over the years I have used Omnifocus, TaskPaper, Paperless, and now Todo.txt. I have found that -- for me -- text-file-based apps are the best (TaskPaper, Todo.txt). They both support tags/contexts (the @ sign) and projects (the + sign in Todo.txt; a string followed by a : for TaskPaper). I can open them in any text editor, or I can manipulate the text in supported apps. (Jesse Grosjean removed his TaskPaper app from the iOS App Store, but fortunately Ole Zorn created an excellent TaskPaper module for Editorial.)
Some actionable tasks need to be done at a very specific time, or by a very specific time. "Mail the DVD at 8:30am" or "Go to Trader Joe's at 6pm." These I put in Due or Fantastical/iOS Reminders.
These are items that I want to consume: books, movies, music tracks, groceries. None of this is urgent (well, except for food). These items do require checkboxes, because once I've rented/downloaded/borrowed/purchased the item, I don't need to do it again (... except for food). I am still using Paperless for this, because the app provides a note field where I can include all the meta info I need (URLs, for example, or who suggested a particular book). And in Paperless, I can uncheck a grocery item to re-add it to my shopping list.
I have a list that is more-or-less called, "Things I Need to Remember to Do at Home to Avoid the Wrath of My Wife." Another is "Lunch Ideas." These items should not have checkboxes, because they are reference materials, not one-time (or even recurring) tasks. Right now I have these lists in Listary which pulls notes with a specific tag from Simplenote. You can toggle a setting for a list in Paperless to remove checkboxes and just use the list as a reference. I have also used Carbonfin Outliner with the checkboxes toggled off for these types of lists.
Of course, one can store all these lists in simple text files and store them in a single directory. nvAlt fans do this. But am I either in front of my phone or a work computer, and I cannot sync Dropbox at work. (One can sync an nvAlt folder with Dropbox.) Although I feel too spread out with my various list apps, I do believe that the ultimate test is whether my system supports both "brain dump" and "information access." Can I quickly note down an idea or todo? And can I easily find it later? Part of my problem is that I don't always recall where I put a todo. With this three-part categorical division, I hope I can better recall a todo's location. If it's actionable, it's in Todo.txt or iOS Reminders; if it's about something I want to buy, it's in Paperless; if it's an evergreen list, it's in Listary. We'll see how it goes.