In C:\Documents and Settings\<your account>\Application Data\Thunderbird\profiles\<8 random chars>.default look in the Mail and ImapMail folders. Do you have folders in those for your accounts? If so, look in them for files such as INBOX and Sent (case doesn't matter). If you have those, and they have non-zero size, you probably still have your messages. With Thunderbird NOT active delete the corresponding .msf files. That is, delete files such as INBOX.msf and Sent.msf. Then fire up Thunderbird (it will recreate the .msf files) and see if you have your messages.
If the files/folders were actually deleted you'll have to try some Data Recovery program or service. If they were deleted stop using that computer, as all activity increases the odds that the actual data is overwritten.