jsfiddle
On JSFiddle, you have your own private Fiddles (on your 'Dashboard'), and you have Public Fiddles.
The Fiddle seems to go Public as soon as it receives a Title.
I want to know the following:
It seems that this is a caching problem. I just refreshed the list after several minutes and the script no longer appears in that list.
To remove a JSFiddle script from your public profile:
As @zalun noted, the script is still accessible by anyone that has the URL to that script. This solution will simply remove it from your public profile.
If it's one of your own fiddles it displays on your dashboard. There you'll see latest revision with a link.
EDIT: The GUI is updated but the functionality seems the same in this matter.
Best Answer
Bit late I know, but I came across the first part of this problem myself today.
In Fiddle Meta, on the left hand side of the fiddle, you can enter a description. This will be displayed under the private fiddle code in your dashboard, so you can keep track of the fiddles.
Don't enter a title in the Meta area, unless you want the fiddle to be made public.
I can't see anyway to re-organise the list of private fiddles, however.