Nothing has broken or gone out, but it is full of issues.
Once I put 1000 miles on my truck I started to have issues. First is the engine. It makes an extremely annoying ticking sound at 1500RPMs and 21RPMs. I brought the truck in to the dealer and told them I thought it was a piston slap or a lifter tick. He got a tech to come out and listen to it and immediately stated he thought it was a lifter... but once he found it it was under warranty, the sound was normal and I shouldn't worry. I have since brought the truck in about the noise several times and each time they say it is normal. I finally wrote Toyota and told them of my issue and their response was take it back to the dealer. I paid 26,000 for this truck. That is a lot of money for an engine that makes so much noise you hate to drive it. The engine also doesn't get very good mileage. I get about 16.5 on the freeway and about 14 in the city.
I have the access cab model and at about 3000 miles, the rear suicide door on the drivers side started to make a knocking noise whenever I hit a bump or dip. I can't get it to go away and when I brought it to the dealer they said they could not duplicate the noise so nothing can be done.
The clutch on this truck is now making a creaking noise when I let it out which is also very annoying. Also if I don't drive the truck for a few days the truck has horrible chatter for the first few miles.
I am the type of guy that hates any ticking, creaking, knocking, or popping noises in a vehicle, and this truck has them all. It has been reliable and I have never broken down though. If you are looking for a reliable truck and are not bothered by noise it will serve you well, but if you hate noises, you will hate this truck.
Sorry to hear of your difficulties with your 2006 Taco. I have an automatic access cab 2006 and have had no problems thus far except vibration due to lousy OEM tires. I had 3 of them replaced under warranty. I just got back from a three state trip and averaged 21 mpg highway. I run mobil one advanced synthetic oil in it and it seems to like it. I believe there are good trucks and bad ones that come off the line (all makes) If you have persistent problems, you have to get in the dealers FACE, because most of them are a joke once they have made the sale. Go in there mad and loud so other customers hear you. It worked for me on the tires. I had the manager ride with me to prove my point and the owner of the dealership call me on the phone to kiss up after I wrote a scathing letter to Toyota Corporate about my lack of happiness with this dealer. The squeaky wheel gets the grease.
First your gas mileage issue may be due to the grade of gas you're running in the truck. The 4.0 V6 is designed to run on high octane, I think the owner's manual recommends 93. If you are running 87 in your tank your gas mileage will suffer, and it may also be contributing to your engine noise.
I've notice that my 2005 Tacoma also makes a clicking sound sometimes when running. However until something actually goes wrong with the motor it doesn't bother me. Some motors just sound like that. I'd have the clutch checked out though, might need some lube.
Concerning the knocking coming from your doors, have the dealership check out the seat belt retractors. I had mine replaced under warranty and was told by the service guy that it was a common problem.
Good luck with your truck. I hope a few odd sounds, most vehicles develope them sooner or later, doesn't turn you off to a good vehicle. Personally I'd much rather put up with the few odd noises my Tacoma makes than the high repair bills owner's of lesser quality vehicles have to deal with.
I am the one who made the original review and would like to respond to the comments. Since day one, I ran the highest grade gas (91) and filled only with Chevron. I tried going to a lower grade to see if my gas got worse or the engine louder. Both happened. The noise doubled in intensity, and I got 50 miles less than I normally did on a tank. One time of that and I went back to premium grade. I since sold the truck, but I would still consider buying a Toy if I had a different and better dealership close by. Too many noises to make me feel comfortable on a long trip.
Why on Earth would you consider buying ANOTHER gas guzzling, poorly made lemon?
2006 Double Cab Prerunner.
A/C blower broke, mud flap broke-off, center storage open button fell off, left foot rest broke, the battery leaked acid and may have damaged the positive battery wire harness, estimated replacement cost $3000.
All automatic door lock actuators broke ($300/each).
All minor except the battery cable.
The truck drives great but was made with cheap parts. This was my third Toyota truck and it may be my last.