For me the inbox is a place for collecting my thoughts to get them out of my mind. It is not a place that I look to to find my next actions. I would like to be able to easily find my inbox when I have thoughts to get out of my head.

Once stuff is in the inbox I leave it there until I am ready to process it. When I process it, I assign each thought a context and a project. Processed in this way it is ready to move out of the inbox. Thus for me I would like it to move when I confirm that I have chosen the right context and project which I guess would be like a "process inbox" command.

As I do not do the items that are listed in my inbox I would not ever need to mark one off as done. I do items that have been processed (assigned to a project and context) and are on my context lists of next actions.

If I enter the item along with its project and context using Quicksilver or the quick entry dialog it does not need to go to the inbox because I have already processed it. Therefore it should go straight into the project. However I don't see myself using this capability often as I have found that the more I separate collecting from processing the more I am free to clear my mind. I can just put the thoughts into the inbox and take the time to process them later. It is really a two stage process.

The logic of ThinkingRock where there is one screen for collecting thoughts and another for processing works for me and cleanly separates the two steps. As I tend to do lots of things at the same time this separation of the steps is a real beneficial discipline for me.