I don't personally view 3-D as a revolution in visual media, but I'm also not ready to just glibly dismiss it as a passing fancy, and I firmly believe that it still has a lot of as-yet-untapped potential. I think 3-D should hold more meaningful applications for gaming than for film, and I even believe that it could be more gracefully implemented than motion controls. Motion controls tend to be a disaster when lazily forced into traditional gameplay models, and even the more groundbreaking Wii Sports titles haven't really entertained me as well as good traditional games. But I can think of a couple existing games that could be subtly yet significantly improved by 3-D.
(This can probably be applied to the original Contra as well, but I'm sticking with Contra 4 because it's fresher in my memory.)
As in the first Contra, there are stages in Contra 4 that switch you to a behind-the-back perspective. Forward progression is automated, so the player is only really running or jumping side-to-side while fighting the enemies ahead. Most enemy attacks are best avoided by dodging left or right well in advance, but there will be moments when you're faced with a row of barrels rolling toward you that spans the entire length of the stage.
Ideally, you should just fire on and destroy the barrel in your immediate lane, but if you're too slow on the draw and don't have enough firepower, you may have to jump the wall of barrels as it passes into the foreground. This can be somewhat tricky because it is harder than it should be to spot how near or far the barrels are from you. You know that the player character is in the foreground and the barrels' origin point in the background, but with only the illusion of depth achievable on a flat image, it can be difficult to track the barrels as they move between layers. If you jump too early, you may just land on the barrel, whereas if you wait too long, you'll be dead before you leave the ground. Also keep in mind that there will more than likely be additional pressure coming simultaneously from enemy soldiers firing bullets at you. With 3-D to make the barrels and other active elements pop out better, there would be less needless guessing and, consequently, less frustration.
Star Wars Rogue Squadron II: Rogue Leader
This is like the previous example, only to a much greater and more serious extent.
In the Rogue Squadron games, you are always flying forward from a behind-your-craft perspective, so that false depth is an ever-present issue. But it is never more a hindrance than in the Death Star stages in Rogue Leader. The first one has you making the classic trench run, just like in the first movie, only now they've added all sorts of pillars and crossbars to get in your way.
Death usually accompanies any impact, and, at the speed at which the game moves, you're not left with much time to gauge where these obstacles are and dodge accordingly. Unfortunately, even though Rogue Leader is built on polygons, everything still looks pretty flat on the TV screen, and thus it's harder than it should be to pick out those hazards as they approach. Essentially, they are like the barrels from Contra 4, but faster and more numerous.
Actually, any basketball game could benefit from 3-D.
Back in the day, in most any basketball game out there, I could probably have gone through the season mode and averaged 200+ points, 40+ steals, and maybe even 4-5 blocks (that's only counting blocks by me, not my AI teammates) in five-minute quarters. The one category where I always performed below what was realistic, however, was rebounding.
In my defense, I tend to have a high shooting percentage, so there aren't many offensive rebounds for me to go after. Meanwhile, on defense, I try to always get the steal before my opponent can even attempt a shot. But the real problem is that, once that ball graphic is in the air, it's always very difficult to track its position in the pseudo-3-D space. In the older 2-D games, part of the problem was that the ball sprite itself often would not scale according to its distance from the foreground, but even in the polygonal games, it's again that issue of multiple planes of play effectively having to be pancaked onto a flat screen.
Of course, I have no desire to see 3-D completely take over, or even to see games that require 3-D. It should never detract or distract from the core experience of a traditional game. But 3-D can help sometimes, or at least it can be a nice bonus, should the player choose to take advantage of it. Like surround sound.