Liset van der Laan: One of the best museums in Utrecht. Check their program before you go because they have very different exhibition, due to their five main collections.
Nina del Rosario: museum with a great set of bizarre musical instrument auto-play contraptions... many things seen that i didn't realise existed. perfect for music and engineering geeks.
Smokingbeest: Not just a bunch of aircraft and tanks, but a beautiful relevant and interactive experience in a brand new building. Located on the former Air Force base Soesterberg. Really worth a visit!
Dima Sh: The biggest castle in the Netherlands. I did not visit it inside but it looks so great from outside and the park is so big and with deers that you won't regret to spend 4 euro