The Google team about a year ago added IMAP services to gmail. This is a great way to be able to manage your mail from several different places (e.g. client software at work, and web based gmail page on the road) and have everything automatically be in sync.
I’m also a big fan of the open source Thunderbird email client. But there is one annoying thing using these two together: when you have a message selected and press ‘delete’, normally this sends the message to Thunderbird’s trash (which completely removes it from Gmail), but in this case, you want to send it to Gmail’s trash.
There was a configuration setting you could try, to send the message to [Gmail]/Trash, but Google doesn’t recommend it (see ‘UPDATE 2, Nov 8th’ here). Instead you are supposed to move (e.g. drag-and-drop) the message to the [Gmail]/Trash folder manually. Well, that’s not too convenient when you have a lot of folders. So, what I’ve found is an add-on QuickFolders which will easily make a shortcut to that folder (and others) so that you can more easily drag-n-drop to send that message to gmail’s ‘Trash’.