Well, some knockup abilities have some form of secondary CC attached to them. Nautilus' ultimate stuns its target for between 1 and 2 seconds after the knockup, for example.
For the rest, it's important to distinguish between knockUP (Janna's tornado) and knockBACK (Janna's ultimate). Knockups are a single form of CC that prevents you from using abilities or moving. Knockbacks, on the other hand, have two parts: the motion and a stun that goes along with it and lasts for the duration of the motion. Under normal circumstances, this makes no difference, but under certain circumstances you can separate them. This is why it's possible to cleanse/flash or QSS/flash out of Blitz pulls; the cleanse or QSS removes the stun, and then you can flash freely. The other main circumstances is when something (a wall, usually) stops the motion. If Alistar headbutts you into a wall, the motion stops, but the stun that accompanies the motion still runs its full course, meaning that you get stunned for a little bit on impact.