I think Duet is the best as well, though I also like Drumhead, that would be my second favorite. The worst has to be A Night in Sick Bay, where Archer acted like a childish lunatic for the whole episode. Good bottle episodes forgo special effects and focus on interesting situations and character studies, bad bottle episodes seem like pointless filler and have the characters involve in insipid plots because they couldn't get the budget to do something better.
Is that really a bottle show. Bottle shows are usually effects lite, use standing sets, and have maybe one or two guest stars.
Going by the list at http://en.memory-alpha.org/wiki/Bottle_show, I'd pick TOS: The Doomsday Machine as the best bottle show, since it's my all-time personal favorite episode anyway. A runner-up would be TNG: The Offspring. Quite a few of those totally suck, especially TNG: Shades of Gray. However, I'm not convinced that that list is entirely accurate or complete. Further discussion of bottle episodes can be found at http://tvtropes.org/pmwiki/pmwiki.php/Main/BottleEpisode.
Bottle shows are awesome. The Doomsday Machine. The Ultimate Computer. The Offspring. The Drumhead. The Immunity Syndrome. The Corbomite Maneuver. Duet. Charlie X. The Changeling. Lots more.
I like a lot of bottle shows, but one that does not work for me is TOS "The Mark of Gideon." (Spoilers) The gimmick of building a fake Enterprise could not work, because the aliens would not have such detailed information, and even if they thought they did, it would never be exact and particularized enough to fool Kirk. And it would not be done, because the aliens would have alternative ways of bottling up Kirk that are immensely faster and cheaper than building a huge starship interior. But what was wildly impractical and expensive for the Gideonites was transparently easy and cheap for the show.
The caveat to "Shades of Gray" is I don't consider clips shows to be bottle episodes. They're glorified "previously" teasers. And there's never been a good one. Ever. SG1 had a borderline "okay" one every now and then. But they had so many it was more a matter of probability. Trek only dared try it once and it was so bad they stayed away permanently.
But it is a bottle show. No guest stars, no real FX heavy bits and the only new set is a bunch of plants on a soundstage. How is that not a bottle show?
Not sure if that would count. Sure, there were no new sets, but a lot of extras in rather elaborate make up. Indeed, the only reason that Sarek and Amanda didn't beam aboard was because the budget had been blown on the make upo and extras, so they had to re-use stock footage of the shuttle from The Galileo Seven.
But the opening scene in Shades' is of Riker off the ship, down on a planet, where he gets stung/bitten. So not a bottle show at all.