There's obviously several others, but these three specifically come to mind. Though, I suppose I haven't actually played too many games with cinematic cutscenes--not as many as most people, anyway--so I didn't have too large of a selection to choose from.
The Great Invasion (Super Smash Bros. Brawl)
Seriously. What is the deal with that ship? So ****ing badass. That subspace weapon? It's like straight outta Star Wars or something. I love it.
Mist's Disappearance (Rune Factory Frontier)
Frontier was the first RF game to start having "anime-esque" cutscenes aside from the game openings, but for the most part they usually pertained to the bachelorettes' introductions and marriages. This was one of the few ones that actually focused on the plot, lol. I think the effects are fairly well done. Also, Gelwein. <3
The Majesty of the Reformed Triforce (Hyrule Warriors)
@
19:05 -
21:06
I tried to find a clip of this specific cutscene, but I couldn't, so, blah. The coloring is a little too gaudy, yeah, but I really like the transformation sequence. The panning across the Bridge of Eldin was what did it for me. Gods, that was so perfect. I wish Cia didn't make such constipated noises at the end there, but ok.