This article give a great overview of Getting Things Done using Thunderbird and other email clients: 

I’ve assigned my labels as follows: Delete, Archive, Action Required, Wait, Defer. Since Thunderbird assigns these as keyboard shortcuts (1, 2, 3, 4, 5), I can go through my inbox and quickly triage items with an appropriate label. The color coding makes it easy to pick out stuff that needs attention.

You can do similar things with Apple’s ‘Mail Tags‘ or using ‘Categories’ in Entourage or Outlook.

Read more: Using Thunderbird to Get Things Done