A thumping heard and felt in the floor is often caused by failing engine mounts. A failing mount allows too much movement of the engine, and will require replacement.
Problems for specific Nissan Quest years:
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Most reported 2006 Nissan Quest problems
The exhaust manifold often warps and cracks, breaking off the studs between the cylinder head and the exhaust manifold. The noise may be most noticeable when the engine is cold.
A creaking or clicking heard while the vehicle is accelerating can be caused by dirt and corrosion build up between the splines of the front hubs and CV axle shafts. Removing, cleaning, and applying a light coat of grease on the axle shaft splines will commonly correct this concern.