I have had a few bad weather flights, but only 2 where I felt particularly scared that something may actually be going wrong.
The first was a few years ago flying HKG-ICN on a JejuAir 737 (which was still decorated in its former owner's branding in the toilets, that being Ryanair). It was not very rough but at night time and even at cruising altitude we seemed to be in the very dense cloud for most of the flight. The wing landing lights kept coming on sporadically, which seemed very odd when in the cruise and I couldn't work out why they would be doing so (does anyone know why?). It may not have been anything out of the ordinary, but I have been on hundreds of flights, most of them at night and I had never experienced that before or since. There didn't seem to be any kind of pattern with the light flashing, which made me think it was something going wrong with the electrics rather than a pilot controlling it.
The second time I felt uneasy was on an Air Asia flight from PEN-KUL last year. We seemed to climb at an incredibly steep angle on takeoff from PEN. It was much more noticeable than any other flights I had been on. The cabin did shudder a bit too and some people around me looked a bit concerned before we eventually leveled out. I really did feel like the captain was trying to get us vertical.