I owned a 2009 Regular Cab 4x4 with the manual transmission. I bought the truck in June of 2010 and sold it in August of 2012. My trucks drive shaft/transmission rattled when the truck was on bumpy/unpaved roads when the drive train was unloaded.
I brought the truck to the dealer under warranty. The dealership (Scranton Toyota) really tried to fix the problem. They kept the truck for three days and attached a chassis ear to try to pinpoint the rattle. The best they could do was to replace the drive shaft which didn't help at all. The service adviser told me that Toyota is aware of the issue and it only affects the Regular Cab 4x4s with the manual transmission. They haven't found a fix for it that I'm aware of.
My truck also had the droning noise coming from the drive shaft that is referenced in the threads above. The problem never got any worse over time but it never got any better either.
In addition to the threads above I also found these other threads when looking for a solution for my regular cab rattle.
Here's a link to Edmunds.com where I reviewed my time with my 2009 Tacoma.
I hope this thread helps someone down the road.