Thunderbird allows you to apply labels (similar to Outlook flags as mentioned in Using Flags and Rules in Outlook) to emails. Unfortunately only one flag can be assigned to a message at a time (is that a problem or am I trying to be overly complicated?) but the labelled messages are easy to see if you have a full inbox (which you don't of course, do you?)
To access the labels go to Tools > Options > Display > Labels (tab)
I have the following labels set up:
- Waiting For
Unfortunately it would appear that 5 labels are the maximum you can have at the moment, but in terms of GTD this is enough. The only reason I could see you needing more is if you wanted specific project labels or one for personal messages, but then you could always get rid of the "Archive" and "Delete" options.
Getting Things Done with Thunderbird :: Learning to be productive One Day At A Time ::.