The final boss fight from Iji
is what immediately jumped to my mind. It uses 3D space pretty well in an environment that, technically speaking, only really has two dimensions (e.g. the boss flies far away into the background and fires at you from a distance).
There's a lot of really cool boss fights in the Zelda series, as well, a few of which are in a sidescrolly perspective (and not just in Zelda II). Those don't use a lot of fake depth, but they still end up being cool in only two dimensions. If I recall correctly, the final boss in Oracle of Seasons
was pretty neat, and from a side scrolling perspective.
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Haha; that's what I get for using too many words.
So, yes. See that video for reference.
...Oh, and the Contra series; there's fantastic stuff there. I was especially impressed with the bosses in Contra 4