Firstly, any and all RMCs, obviously.
Honestly, I think the Iron Wolf-Apocalypse transformation was quite a good upgrade. New theming, new paint, MUCH smoother, and is overall a much better ride.
I also think that the Demon upgrades are quite overlooked. It may not have been the best choice(taking out 2 killer airtime hills for 2 loops and a tunnel </3), but the theming improved significantly, including quite impressive rockwork, fairly decent lighting, and (when it was working) a really cool waterfall.