I'll start with the disclaimer that I haven't played many 9-holers that were anything special.
A long time ago I played Oregon Park, near Atlanta, when it was 9 holes but 2 very different tees on each. My memory is fuzzy, but says it was fairly good.
Crooked Creek Park - Pro 9 is pretty good, but odd. It's listed as a separate course, but it's really 9 extra holes attached to a pretty good 18-hole wooded course, giving it a few longer shots. It's not really played as a separate course, but as a bonus to stretch the round to 27, or in combination with 9 holes on the original course to make a unique 18. If it were truly a stand-alone 18---and the 9 basket closer to the 1 tee---it might be a 3.0.
My favorite ever shouldn't really count. It was Stoney Hill, somewhere in 2005 or 2006, when it reached the 9-hole stage. It was a tough 9-holer, consisting, approximately, of current holes 1-5, 9, 11, 12, and 18.
Which leaves me with
Sioux Central School , which I stumbled upon quite by accident somewhere in Iowa. It's a 9 holer that's mostly in something of an arboretum, around a pond, very pretty and with interesting shots. It's 11 years old with only 1 review, by, you might have guessed, Martin Dewgarita, and I wrote this post mainly because it really deserves mention. Check out the pictures.