I've been using Trello for a couple of months and so far I've been impressed just how flexible its underlying metaphor is. The implementation itself is easy to use and surprisingly fun. I love the fact that very few things are actually deleted, instead they are merely archived and can be searched, unarchived, etc.

Stuff that I miss:

* Filtering cards based on tags. Once you have a couple of dozen cards on a list it becomes increasingly difficult to get an overview of what you're doing, what you should do, etc. I use tags like DO THIS, DISCUSS THIS, INCOMING and would really like to filter lists so they only displayed, say, DO THIS cards. Right now I find myself fiddling around with the lists far too much, trying to figure out what I should do next. Not good if you're a procrastinator.

* Universal markdown support. Sometimes you can markdown, other times you can't. Confusing.

* More than 5 tags on a card. I think this limitation is arbitrary: Trello uses a color bar for each tag on a card so there's a limit to how many colors, i.e. tags, you can display. On the other hand it forces you to be more disciplined with your tagging, which makes organization and collaboration more streamlined.

* Trello doesn't do traditional, calendar centric, planning too well. Sometimes I just want to move around cards on a calendar (day, week, month). My current solution is to create a card for each week or month but it strikes me as unnecessary manual labor.

* Card comments should be editable once added. Currently, if you discover an error in a comment, you have to delete the comment and re-add it.