Just a few things that popped to mind immediately -
ISO. An entry-level dSLR is going to have visible noise even at lower ISOs - like 400. Higher ISOs will show noise to the point that the image quality is greatly effected. The higher end/pro cameras, otoh, will show much less noise at every level and be more usable at higher ISOs....regardless of the lens being used.
Different cameras also vary in the number of available focus points. So, you could have a camera that only has 3 or 5 focus points, and a camera that has 50+. The same shot could come out completely different b/c the higher end camera is going to be able to pinpoint a much more specific focus point.
Lenses...well the difference can be the earth and the sky. A kit lens that runs f/5.6, even if it's set at 50mm won't give you the same rockin' bokeh you would get from a 50mm prime lens - like a 1.8 or a 1.4 - b/c of the difference in aperture settings. (Bokeh, if you're not familiar, is the term for the blurred out background in a photo.) The speed of the lenses (smaller f#, faster lens) also effects ISO & shutter speed, so really, that can make a world of difference when it comes to how the photo is actually taken.