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I've tried several times to move my personal organization system to Remember the Milk, because it has rich support for three features I really like:

  • keyboard: just about every field has a keyboard shortcut, which makes entry and maintenance very efficient
  • tags: clearly visible, clickable, and there's a separate management screen
  • searches: mix and match most attributes, boolean operators, and save favorite searches

Unfortunately, the web-app has been all but abandoned, going without even bug fixes. Is there another application that has these features, either on Linux (perfect!) or the web (acceptable)?

[EDITED TO ADD]: Web-app recommendations also need to include two-factor authentication that doesn't require a smartphone. I apologize for not including this in the original post, but it didn't occur to me that this would still be an issue in mid-2015. :/

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    I just saw your edit and updated my answer. Please leave a comment on the answers whenever you add essential information to your post so that other users will have a chance to update theirs – Tymric Jul 7 '15 at 10:56
  • Because it wasn't requested in the original post. And since StackExchange doesn't notify the answerer whenever the question changes, the asker should do it manually by comments, or post a follow-up question if the feature is important enough – Tymric Jul 7 '15 at 14:20
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Toodledo

I was using Remember the Milk my self a little on and off, even had a premium subscription for a year. Today I'm using Toodledo and it seems to fullfil most of my needs, and according to your current list most of yours.

  • The main screen displays most keyboard shortcuts, but you can press ? and get all of them in a popup window
  • It has tags, and a separate organize tags window
  • And it has a rather powerful search enginge with the possibility to save searches, and it also supports filters

In addition to being a good task organizer, Toodle do also has both outlines, notes, lists and habits. All areas I like to have joined in one tool. And you can customise the fields of the tasks to your likeing, and can choose from fields such as: Folder, Context, Goal, Start Date, Start Time, Due Date, Due Time, Repeat, Length, Timer, Priority, Tag, Status, Star, Location, Assignor, Trashcan.

I also like the fact that multiple apps (for both ios and android), browser plugins and desktop applications are using the toodledo api, meaning that you can choose from a variety of access point to access your toodledo account.

The free version is fully functional, albeit limited in the number of lists and stuff, but there is no such thing as a free lunch. And there seems to be an active community around Toodledo, both the main developers and developers for 3rd party applications.

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Todoist

I use Todoist as a personal organization and project management tool. It is free to try, but most features require a premium subscription. It supports your requirements as well as many other features:

  • Keyboard shortcuts for entries, editing, formatting, and search
  • Tags, referred to as labels. Visible, clickable, and with customizable color coding
  • Searches, called Filters accepts natural language for dates, mixing of project and label attributes, and use of boolean operators

Todoist does not currently have a Linux app, but it has web apps, as well as Chrome and Firefox extensions. Here's the current list of supported platforms:


Edit re 2-factor authentication

While still not natively supported in Todoist, you can use two-factor authentication by activating it in Google then logging in using your Google account

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I find the Nirvana web app (and iPhone app) really good, with great support for keyboard and tags

https://www.nirvanahq.com/tour

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You can use an open source Nitro service, which provides a slick interface, lists, tags, keyboard shortcuts and search. It has a web version, Linux and mobile apps.

Alternatively, you can use a closed source Wunderlist.

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