It's been almost one year since I purchased my 06 TRD Crew Cab Short Box and overall it was a great buy. It has been very reliable, gets relatively good mileage (at 11.2k miles, I've averaged 17.75 MPG) and is fun to drive.
Go anywhere ability - I hunt in very remote places and this thing is impossible to get stuck. Surprisingly strong engine, yet it gets very good gas mileage (20.2 is my best to date).
Tailgate: isn't strong enough (thin sheet metal) and needs to be reinforced in future models. Accessory boxes in back seat should go all the way across to accommodate long items. I wish there were a few more options (sunroof, navigation, etc.) so I could get a factory installed accessory.