I was a long-time Toodledo user but gave it up last year for a variety of reasons. Over time I simplified it just as SherGTD mentioned (e.g. status field, priority, etc) to remove the clutter and make it simple to use, but in the end a few things really bugged me:
1. No real inbox - the equivalent is 'No folder' which just annoyed me
2. No drag & drop other than in subtasks
3. No manual ordering of tasks
As others have noted, subtasks can be a challenge to handle in Toodledo depending on your settings.
There is an online solution named Nirvana (www.nirvanahq.com) that was built for GTD methodology. I'm not using it but it has many loyal users and they have a feature to flag projects as active or inactive. Might be just what you want.
I'm using Appigo's Todo Pro which is an online system (similar to Toodledo) but with the features I need (inbox, manual sort, drag & drop, etc). They also have native apps for iPhone, iPad & Mac. I use the online version at work (Windows environment) and iPad or iPhone most other places. It's not specifically GTD but handles my workflow well and has plenty of features, many of which are not obvious at first glance because of the minimal UI style that Appigo adopts.



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