Sperm swim, airway and oviduct epithelia move mucus using motile cilia (which is identical to a flagellum). The blastocyst uses nodal cilia (which twirl) to differentiate left and right.
Most mammalian cells have a primary cilium which (it is hypothesized) is used to sense the environment. The mammalian cilium is identical to the bacterial flagellum, and the protein machinery associated with the growth, maintenance, and secondary signalling pathways is highly conserved.
There's obvious differences between prokayotic and eukaryotic cells- in addition to size (bacteria are much smaller than protozoans). The presence or absence of a nuclear membrane, the structure of the cell wall (gram positive or negative), but metabolic pathways are conserved, DNA is DNA everywhere, ribosomes are conserved, the ER is conserved, etc. etc. Bacteria do not have
mitochondria.