How many miles on your vehicle?
Sounds like suspension and the bad reactions from going over speed bumps is almost surely bad shocks. But, squeaks as you go over speed bumps could be a bad joint or bushing in the suspension, which would make the clunks/thuds. Sway bar bushings wear out as well, they will make a noticeable clunk as the vehicle sways one direction to the other, i.e. the bar shifts within the bushings and clunks when its stopped.
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