Hm. Making a Minecraft prison...
Well you can't just make the typical locked building, since with enough time inmates could break down the walls. You could have guards to try and prevent that, but they would have to resort to force in the end, so any sentence would likely end up as capital punishment.
An effective system of long-term containment is going to have to rely on cobblestone, or something else that can't be harvested with bare hands. Otherwise, there really is no way to keep someone somewhere. I presume you're going to want to be able to access your prisoner at some point. If you DIDN'T need to keep access to them available, you could probably build a small cell and submerge it in lava. OR you could have some fun and build an extremely tall 1x1 tower, put the prisoner at the top, and then remove all the blocks underneath the top one, leaving them suspended in midair.
If being able to access and monitor the prisoners IS a necessity, I'm think a pit trap of some sort might be best, probably with a lava moat. It would have to be at or near bedrock though, to keep inmates from tunneling under the lava. This way you can also maintain access from catwalks overhead.