There are plenty of 2D games that have tried to make themselves look 3D. Can you think of any games that could be simulated in a more 3D-looking format using only isometric graphics, or do you know of any? I think the main point would be that you would control a character by moving the angle it's facing either with the mouse or arrow keys, and then moving it forward.

In my opinion, a star-ship shooter would do well as you changed your ship's pixel_z and fired off projectiles at other ships on the same altitude as yourself.
Haven and Hearth, check it out.

So a star ship shooter would actually be horrible for isometric because you'd have a really poor job of being able to predict where your shots are actually landing and the game Hatred is a good example how to fuck this up in 2D, let alone 3D.

The important thing to remember is isometric perspective allows you to make a game LOOK 3D, but it's still essentially a 2D game.
I'm having some difficulty understanding what it is that you are asking. Do you mean 3D-looking format as in an original StarFox sort of way? The way that it simulates a 3D environment? Or are you specifically referring to having 2D graphics that look 3D like Donkey Kong Country?

Or are you perhaps specifically referring to the way that the game controls?
In response to Lilius
I would simulate 3D graphics by allowing the ship to rotate its angle, go in any direction it wants, raise and lower its altitude in the isometric perspective, and fire off projectiles at any angle.
In response to Kidpaddle45
This game is god tier. In fact, I never completed it. Might have to play through again...
So you're pretty much talking about but with some Z axis that you can freely accelerate along?

Isometric tends to have some depth perception problems, which is why you generally see isometric games have relatively simple or flat level layouts.

Diablo II (and by extension, Diablo III) essentially have flat, plane-like levels.
Starcraft 1 is like this as well.
Isometric space games, like what I had linked above Andromeda, or others like Escape Velocity Nova, also essentially has a flat level.

This is also a problem that is seen in just about any 3d game with an overhead perspective, like Warcraft 3 and Starcraft 2 and Final Fantasy Tactics.

So how do you solve this problem of perception of depth?
1. Scaling sprites based upon the distance from the view point would definitely help, but might not be enough.

2. Try illustrating depth by showing the location on the X,Y plane, and a line parallel to the Z axis from that point to where the ship is located in 3-space.
Homeworld did this, to good effect. homeworld_sensor.jpg or
I would simulate 3D graphics by allowing the ship to rotate its angle, go in any direction it wants, raise and lower its altitude in the isometric perspective, and fire off projectiles at any angle.

What I'm talking about is when you have something that can be slightly sized up and lowered, with a visual feature that helps signal the altitude along with a counter (So that you don't have to do anything to the size and can keep it the same, this is a trick I've seen in games with ships that use really large shadows and fade them out!) Of course I will sightly enlarge and shrink the ship if needed, but I'm going to try avoiding doing so at first.

So while you alter the ship's pixel_z layer , pixel_y, pixel_y, by using holding CTRL and 1-2 arrow keys to go a specific direction, or just using left and right to change direction and north and south to go that direction. Spacebar would be to fire off bullets that would take up a small diamond and be measured probably in a few small pixel squares for accuracy that are attached together (when one collides it will delete obviously as well)

You'd just have to make some kind of shading and shadow to show you were raising or lowering your ship, I don't think you have to modify the ship's size much if at all (which can be done on the fly and cached probably). I'm imagining these ships flying over a landscape that was essentially the same as a normal one, only rotated for the isometric graphics... with small structures that could interfere flight paths but normally the plane will level out if one attempts to lower the ship too far. Shift + Up and shift+down will raise the pixel_z layer, Left and right will rotate the ship's angle, and Up and Down will be used to put the ship in either forward or backward motion. Space bar to shoot projectiles obviously... that are given a height and displacement based on the players, and will only "collide" with another player (via a layer check ) if they are on that projectile's layer.

I did my best there to explain what I am trying to say .