One problem related to engine knocking noise has been reported for the 2006 Toyota 4Runner. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Toyota 4Runner based on all problems reported for the 2006 4Runner.
Steering has knocking sound while turning left or right, it started at about 62000 miles. Also replaced coil pack #2 and # 4 at 49000 miles had another go out a year later, delership told me to replace the remaining 4 coil packs, by only replacing the corruped one will cause the ohers to fail.