My favorite microbe in the set so far is Biddulphia because the shape is so cute but also because diatoms are awesome. They have glass shells which is awesome and I work with ceramics which has glass components so I am quite fond of it. Their mitosis is also really interesting, and kind of stupid.
Noctiluca is close too because it uses light and gas manipulation, also--cute.
Then I can't forget about the cat flea--not quite a microbe but so awesome, Fleas rock.