Amiga: Battle Squadron supports mouse control, but not proper mouse control. Grid runner has mouse control, and there's Goldrunner ofc. Resolution 101 is 3D, and is actually prrreddy goood.
Windows/PC-DOS: For 3D it's not hard to find, Star Wars shooters are good, there's that space mission one from 1999 or so with Bruce Campbell's voice in it, whose name escapes me.
2D shoot'em-ups with mouse control on Windows? Whoa. There might be a Gridrunner that works in DOSbox I guess... but I think you'll be looking at "Pre-Voodoo gfx cards" era games.