I've got quite a few:
Eejanaika - was a month off opening on my first visit to Fuji-Q, and closed for maintenance (they were planting a **** ing tree from what I could see) on my second visit.
Batman:The Ride at Magic Mountain - I'm actually quite relieved it was closed though because if I would have ridden it, I wouldn't have managed to get on Goliath (just got into the queue before it was closed off at the end of the day). I've ridden two Batman clones; I LOVED Goliath, so it worked out as a blessing really.
Almost everything at Expoland - Orochi (now in France anyway) was down for maintenance. I managed to ride Daidarasaurus, which was ****, but when I finally got off the bloody thing it was pouring down and they'd closed practically everything else. I managed one other coaster, some kiddy thing, and that was it. Again, maybe a blessing since Fujin Raijin 2 actually killed someone the day after I was there.
Everything at Parque de Attracciones - because the website lies and/or they closed everything because of a bit of rain earlier in the day. NOTHING was running apart from one side of the drop tower, even though, according to the website, the rides were operating until 10 or 11pm that day. I arrived at 6, after any rain had well and truely stopped, and got **** all.
I originally missed Black Hole Express, then called Scream Machine, formerly known as Horror Express, and had no intention of going back to the park, but ended up changing my mind and going back, almost 2 years later, just before I left Korea to make sure I got it. I'm glad I did now, as it's probably my favourite Vekoma looper.
Edit - Just looked in the coaster counting topic and remembered that I missed the Toboggan thing at Lakemount.
I'm sure there are others as well, I just can't think of them right now.