I didn't have that issue with Luigi.  I had it to an extent with Revelations which is why it isn't higher on the list.

I haven't extensively used the 3D effect, but out of all the games I've played A Link Between Worlds had the best 3D...

I haven't had that problem in either game.

On Resident Evil: Revelations, did you have the Depth on Normal or Strong or Very Strong (in Options of the game; RE: R) ?

Any game that isn't Pokemon X or Y.

It varied.  I alrernated generally between strong and very strong.  Certain elements, most notably my targeting laser and lights had a double image to them.  In general, the 3D doesn't work well against a black background.  The issue also occurs in Uprising, but there aren't that many black backgrounds in the game.

Yeah, a black background does cause ghosting. In Luigi only the ghost, like the green ones had this problem because the room would become dark, but I just ignore it and played.

I believe Tron Legacy 3D movie had this problem too.

In CastleVania you can turn the brightness to 10 in the options.

This is why I always have the brightness in the Home Menu on 5 (Max).

Playing outdoors in the day time reduces ghost effects if it's not a direct enough hit by the rays of the sun, like playing in the bus and banks.

My new 3d-effect-favorite on the 3DS is "Professor Layton and the Azran Legacy".

That game is a stereoscopic piece of art, each background captures the scenario from a perfect viewing angle for 3d depth perception.

Snake Eater 3D is pretty good as well.