I'm glad to say that's quite easy with CDF, but the cell will only be available to users with the CDF Player installed.
Select the output cell in Mathematica, and go to File > CDF Export > Web Embeddable. Make sure Current selection is selected in Step 2. Choose a location to save the file, preferably somewhere in the directory of your site. The rest should be pretty easy to follow.
If you need the file to be accessible to users without CDF Player installed, you do indeed have to use webMathematica. It looks like the brain-segmentation example uses a combination of webMathematica and a Flash applet.
