true isometric projection with opengl

Try using gluLookAt

glClearColor(0.0, 0.0, 0.0, 1.0);
glClear(GL_COLOR_BUFFER_BIT);

glMatrixMode(GL_PROJECTION);
glLoadIdentity();

/* use this length so that camera is 1 unit away from origin */
double dist = sqrt(1 / 3.0);

gluLookAt(dist, dist, dist,  /* position of camera */
          0.0,  0.0,  0.0,   /* where camera is pointing at */
          0.0,  1.0,  0.0);  /* which direction is up */
glMatrixMode(GL_MODELVIEW);

glBegin(GL_LINES);

glColor3d(1.0, 0.0, 0.0);
glVertex3d(0.0, 0.0, 0.0);
glVertex3d(1.0, 0.0, 0.0);

glColor3d(0.0, 1.0, 0.0);
glVertex3d(0.0, 0.0, 0.0);
glVertex3d(0.0, 1.0, 0.0);

glColor3d(0.0, 0.0, 1.0);
glVertex3d(0.0, 0.0, 0.0);
glVertex3d(0.0, 0.0, 1.0);

glEnd();

glFlush();

Results in

We can draw a cube to check that parallel lines are indeed parallel

glPushMatrix();
glTranslated(0.5, 0.5, 0.5);
glColor3d(0.5, 0.5, 0.5);
glutWireCube(1);
glPopMatrix();

An isometric projection is just a matter of using an orthographic projection with a specific rotation angle.

You should be able to choose any of the 8 potential orientations, with a orthographic projection, and get a perfect isometric view of your model. Just follow the math in your referenced Wiki article for setting up the view matrix, and do an orthographic projection for your projection matrix, and you're all set.

Maybe I'm not quite grokking the math correctly, but couldn't you just position your camera as it explains in that Wikipedia link and use a standard orthogonal projection?

Even if it's not the same, the projection stack is entirely up to you.

glMatrixMode(GL_PROJECTION);
glLoadIdentity();
// your isometric matrix here (see math on Wikipedia)
glMatrixMode(GL_MODELVIEW);

If you do not want to use GLU, here is bare bones using glOrtho

void gl_enter_2_5d_mode (void)
{
    glMatrixMode(GL_PROJECTION);
    glPushMatrix();

    glLoadIdentity();

    double scale = 50;
    glOrtho(-scale,
            scale,
            -scale * 0.7,
            scale * 0.7,
            -scale,
            scale);

    glMatrixMode(GL_MODELVIEW);
    glPushMatrix();

    glLoadIdentity();

    glRotatef(35.264f, 1.0f, 0.0f, 0.0f);
    glRotatef(-45.0f, 0.0f, 1.0f, 0.0f);
}

void gl_leave_2_5d_mode (void)
{
    glMatrixMode(GL_MODELVIEW);
    glPopMatrix();

    glMatrixMode(GL_PROJECTION);
    glPopMatrix();
}

then draw a cube in it

void cube (double size)
{
    glBegin(GL_QUADS);

    glVertex3f(size,size,size);
    glVertex3f(-size,size,size);
    glVertex3f(-size,-size,size);
    glVertex3f(size,-size,size);

    glVertex3f(size,size,-size);
    glVertex3f(-size,size,-size);
    glVertex3f(-size,-size,-size);
    glVertex3f(size,-size,-size);

    glVertex3f(size,size,size);
    glVertex3f(size,-size,size);
    glVertex3f(size,-size,-size);
    glVertex3f(size,size,-size);

    glVertex3f(-size,size,size);
    glVertex3f(-size,-size,size);
    glVertex3f(-size,-size,-size);
    glVertex3f(-size,size,-size);

    glVertex3f(size,size,size);
    glVertex3f(-size,size,size);
    glVertex3f(-size,size,-size);
    glVertex3f(size,size,-size);

    glVertex3f(size,-size,size);
    glVertex3f(-size,-size,size);
    glVertex3f(-size,-size,-size);
    glVertex3f(size,-size,-size);

    glEnd();
}

void test (void)
{
    glPolygonMode(GL_FRONT_AND_BACK, GL_LINE);
    glBindTexture(GL_TEXTURE_2D, 0);
    cube(1.0);
    glPolygonMode(GL_FRONT_AND_BACK,GL_FILL);
}

and call something like this

gl_enter_2_5d_mode()
test()
gl_leave_2_5d_mode()

should you want to toggle between 2d and 2.5d (so you can draw your UI) then I have similar functions to enter and leave 2d mode e.g.

void gl_init_2d_mode (void)
{
    /*
     * Enable Texture Mapping
     */
    glEnable(GL_TEXTURE_2D);

    /*
     * Enable alpha blending for sprites
     */
    glEnable(GL_BLEND);
    glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

    /*
     * Setup our viewport
     */
    glViewport(0, 0, game.video_pix_width,
               game.video_pix_height);

    /*
     * Make sure we're changing the model view and not the projection
     */
    glMatrixMode(GL_MODELVIEW);
    glPushMatrix();

    /*
     * Reset the view
     */
    glLoadIdentity();

    gl_init_fbo();
}

void gl_enter_2d_mode (void)
{
    /*
     * Change to the projection matrix and set our viewing volume.
     */
    glMatrixMode(GL_PROJECTION);
    glPushMatrix();

    /*
     * Reset the view
     */
    glLoadIdentity();

    /*
     * 2D projection
     */
    glOrtho(0,
             game.video_gl_width, game.video_gl_height,
             0, -1200.0, 1200.0);

    /*
     * Make sure we're changing the model view and not the projection
     */
    glMatrixMode(GL_MODELVIEW);
    glPushMatrix();

    /*
     * Reset the view
     */
    glLoadIdentity();
}