Are you asking what the best clone is or what the best software to make a clone is? The best/most popular clone is reddit (came shortly after digg) The best software is pligg id say.
Yes pligg did get sold, but the developement is continuing and it is still free. There are also many active members still in the support forums that help out with all of the bugs. Pligg is probably the most versatile digg-like cms, but it can be buggy to set up, and can give some head aches getting everything going.
pligg is the best one, worth your money if you know how to program and get a lot of websites to join your site.
I found this list on one of DP threads, didn't use it yet * www.Authorcontent.com * www.ChakkdeIndia.com (Indian sites/India related content only) * www.Digg.com * www.Propeller.com * www.Reddit.com * www.Del.icio.us * www.Stumbleupon.com * www.Socialogs.com * www.Indianpad.com * www.Google.com/Bookmarks * www.Technorati.com * www.Furl.net * www.Diigo.com * www.Wirefan.com * www.Bibsonomy.org Maybe it'll help you.