Thunderbirds threaded view is nice but doesn't quite recreate the magic that Gmail's conversation view does. Free add-on Thunderbird Conversations brings Gmail's conversation view (and its many conveniences, like quick reply and contact tooltips) right into the new Thunderbird 3.3.
Thunderbird 3.3 is still in alpha, but if you're feeling a bit daring, you can download it now and install the Thunderbird Conversations add-on to try it out. It's organized almost exactly like Gmail's conversation view, collapsed into one box showing the latest messages and previews of the ones above it. You also have an inline reply box at the bottom of the pane as well as contact tooltips just like Gmail's if you have the Contacts for Thunderbird add-on installed. It really makes Thunderbird cleaner, easier to use, and more Gmail-like, so it's definitely worth trying out if you're a fan of the Gmail webapp.
Thunderbird Conversations is a free download for Thunderbird 3.3.