Intermittent rear passenger clunking sound

SOURCE: front suspension

it could be the sway bar bushings

SOURCE: 2006 toyota sienna thumping noise on drivers side

Has the upper strut bushing been replaced? Have you checked to see if the wheel is loose? To do so jack up the side you here the noise on and use a tire tool or piece of pipe and jack up the wheel when till it's off the ground about an inch enough to get you bar under the wheel. Next pull up on the wheel with the bar if you feel a clunk then get a second person to pull the lever up and down and see where the looseness is, if there is no looseness when prying up and down then you will have to wiggle the wheel from left to right to see if you can find the noise, a also you will have to pull on the drive axle to see if it's loose once you determine what is loose then you can tell me and I will tell you what has to be replaced.

SOURCE: thumping noise in front drivers side wheel and

Check your suspension bar and check your front strut assembly, jack up the side you here the noise on and pry against the tire to see if you have any movement between the strut housing and the frame, make sure the top strut nuts are tight, if they are next check tie rod ends to see if you have any play, next pull the wheel from the top and bottom to see if it's loose if it is watch while someone else wiggles the tire, you could have a tie rod loose or a king pin loose. Also it could be a wheel-bearing nut. Let me know what you find so I can tell you how to replace it.

SOURCE: Metallic "clunking" noise from right front end

sounds like the top plate for the strut is bad, i beleive you may be able to just replace the plate and not the whole strut ,

SOURCE: I had a clunking noise

never, I've seen them rust off. and there should be no reason to move it for a break service.