A suggestion from someone who uses a similar system: get rid of yellow flags, and simply move those emails to whatever archive folder the "completed" emails would go to. A task where you're waiting for input from someone else is a task for that someone else, not for you. As such, it has no place in your inbox.
All in all, using inbox as a TODO list has been a great arrangement for me - both at work and privately.
In that case, if it's something they need, you can forget about it. If, on the other hand, it's something you need, then you need to treat the e-mail as a reminder that you need to follow up - essentially, another item in your TODO - so it needs to stay in your inbox.
Well, I wrote "you need to", but I'm describing what works for me. :) YMMV, obviously.
All in all, using inbox as a TODO list has been a great arrangement for me - both at work and privately.