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Puppy Linux has 3 flavors available.

I am looking for some differences between the three. This way I can make an informed decision on which to go with, instead of randomly picking or just getting the smallest one.

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It is better to clarify for what purpose you need puppy, For example I have a old laptop which inspired by Puppy wary where as I installed puppy lucid on it before, but consumes more resource than wary. It support DEB packages, also as did lucid Puppy. – hassan_noori Jan 5 '13 at 8:43

Spup (Slacko)

Spup is the generic name for puppies built with Slackware binary packages. The main reason behind Spup is binary compatibility with Slackware packages, and the Puppy Package Manager can install from any of the Slackware repositories. The foremost Spup right now is "Slacko", and is currently one of our official flagship puppies.

Upup (Lucid, Precise)

Upup is the generic name for puppies built with Ubuntu packages.What you get is a very small distro (the live-CD is about 130MB) yet with just about every application you would need and the speed and ease-of-use that Puppy is famous for. All of the advantages of Puppy, plus binary compatibility with Ubuntu .deb packages -- Puppy's own Puppy Package Manager will install any packages from the vast Ubuntu repositories!

Basically a Upup is a Puppy that has some compatibility with Ubuntu. Typically produced using Woof with Ubuntu packages. Often they are named after the Ubuntu version name, for example Lucid, Jaunty and Precise

And between Spup and Upup it is your matter of choice. see this Why Slack instead of Ubuntu

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up vote 0 down vote accepted

Slacko Puppy is larger but includes Firefox

ISO Size: 165 MB

has the latest Firefox browser (other browsers are available through the 
Package Manager);

Lucid Puppy is smaller but Firefox must be downloaded

ISO Size: 132.6 MB

allows the user to install his/her favorite browser (user installs it from 
the Internet at first boot).
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