Well, having a little spare time I'll show you a pretty neat way to do this. This method allows more control over your model when it comes time to texture. The overall process isn't very difficult, you just have to use a few tools at your disposal, namely insert edge loop, merge edge, and extrude. First with your cube you'll want to use the insert edge loop tool near the edges of your cube, kind of like framing it. This is so when you smooth it or convert it to subdivisions, the edges of the cube will remain square. I've put some cylinders in as a reference for where to put the edge loops.
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Continue using the insert edge loop tool to make a square around your reference object.
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inserting more edge loops for the second hole
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Now that all the polygons are in place, select the faces where you want the hole to be. Make sure to select both the top and bottom faces, then extrude
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Now, when you extrude the first time, you'll want to scale the faces, not move them. Click the cube portion of the manipulator to make the center scale handle show up.. I can't think of a better name for it right now, so that's what i'm calling it. using your center scale handle, scale inward just slightly, hit extrude again, then move the face inwards slightly, extrude again, and move the faces toward eachother.
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Once you get the faces moved close to eachother, delete the faces, go into wireframe mode (4 on the keyboard), select your polygon and go to the merge edge tool. the edges of the hole will look thicker because those are the only ones you can merge together. Connect them up, one pair of edges at a time.
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more detail
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Once you have your hole or holes closed up, it's good to go for texturing or conversion to subdivisions or smoothing. You can hit 5 to switch back to shaded mode.
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After converting to subdiv, hit 3 to refine the mesh and voila! those square holes are now round! Here's a quick render of the final product.
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I hope this helps! Feel free to drop me a line or add me to your friends list.
