How to render a colored 2D rectangle.

There's no need to create the whole texture (as of Unity 4). This works as expected:

 void DrawQuad(Rect position, Color color) {
     Texture2D texture = new Texture2D(1, 1);
     texture.SetPixel(0,0,color);
     texture.Apply();
     GUI.skin.box.normal.background = texture;
     GUI.Box(position, GUIContent.none);
 }

Here's one way to do it with GL.Begin/GL.End. You should also be able to draw a mesh similarly with Graphics.DrawMeshNow. Please select a material that accepts color. I just tested this quickly with GUI/Text Shader but you will probably want to use a solid color shader that uses the vertex color channel.

 using UnityEngine;
 using System.Collections;
 
 public class Example : MonoBehaviour
 {
     // Please assign a material that is using position and color.
     public Material material;
     
     public Rect position = new Rect (16, 16, 128, 24);
     public Color color = Color.red;
     
     void OnGUI ()
     {        
         DrawRectangle (position, color);        
     }
         
     void DrawRectangle (Rect position, Color color)
     {    
         // We shouldn't draw until we are told to do so.
         if (Event.current.type != EventType.Repaint)
             return;
         
         // Please assign a material that is using position and color.
         if (material == null) {
             Debug.LogError ("You have forgot to set a material.");
             return;
         }
         
         material.SetPass (0);
         
         // Optimization hint: 
         // Consider Graphics.DrawMeshNow
         GL.Color (color);
         GL.Begin (GL.QUADS);
         GL.Vertex3 (position.x, position.y, 0);
         GL.Vertex3 (position.x + position.width, position.y, 0);
         GL.Vertex3 (position.x + position.width, position.y + position.height, 0);
         GL.Vertex3 (position.x, position.y + position.height, 0);
         GL.End ();
     }
 }

Create a new folder in your Assets and name it "Resources", put a white texture of any size (32x32 for example) inside and name it WhiteTexture (It can be BMP, TGA, PNG, JPEG...) and do something like this in OnGUI function:

Texture2D MyTexture = Resources.Load("WhiteTexture") as Texture2D;
GUI.color = new Color(1.0f , 0, 0);//Set color to red
GUI.DrawTexture(new Rect(positionX, positionY, sizeX, sizeY), MyTexture);
GUI.color = Color.white;//Reset color to white

This will render a red rectangle.

p.s. I didn't test this code. =)

Drawing a rectangle outline

 public static void DrawRectangle(Rect area, int frameWidth, Color color)
 {
     //Create a one pixel texture with the right color
     var texture = new Texture2D(1, 1);
     texture.SetPixel(0, 0, color);
     texture.Apply();
 
     Rect lineArea = area;
     lineArea.height = frameWidth; //Top line
     GUI.DrawTexture(lineArea, texture);
     lineArea.y = area.yMax - frameWidth; //Bottom
     GUI.DrawTexture(lineArea, texture);
     lineArea = area;
     lineArea.width = frameWidth; //Left
     GUI.DrawTexture(lineArea, texture);
     lineArea.x = area.xMax - frameWidth;//Right
     GUI.DrawTexture(lineArea, texture);
 }

I found a way to draw a box inside OnGUI that only uses a very small texture, and it works on my machine (mac laptop).

I use this to render a 50% transparent white box on the entire screen, including the GUI elements. Just substitute the color values for whatever color you need. You could even make gradients by setting different colors in this 2 by 2 pixel texture.

  void OnGui () {
     Texture2D tex = new Texture2D(2,2);
     for(int i = 0; i < tex.width; i++)
     {
         for(int j = 0; j < tex.height; j++)
         {
             tex.SetPixel(i, j, new Color(1f, 1f, 1f, 0.5f));
         }
     }
     tex.Apply();

     GUIStyle tempstyle = new GUIStyle();
     tempstyle.normal.background = tex;
     GUILayout.BeginArea(new Rect(0,0,Screen.width,Screen.height),tempstyle);
     GUILayout.EndArea();
  }