How to Read PKNA

Here is an overview of PKNA stories that weren't printed during the main runs, and thus could have been missed. All of these are also in the full overview, which will also give away less plot than this page.
Note: stories that are grouped together (e.g. Universo PK) will be linked via their subseries rather than individual stories, since inducks provides a good overview already.

PKNA/PK²'s easily-missed stories are:

PBNA, an 8-page 'parody' of PKNA, with Fethry as the main character.
A set of one-pagers, printed in the Disney MEGAzine (1, 2, 3, 4, The World of PK, 5, 6, 7, 8, 9)
Yearly specials, released in August 1997, 1998, 1999 and 2000. The 2001 special is part of PK².
There's a very early PKNA story titled Incubo Sul Fondo. It was partially completed (fully written, half-drawn) when it was scrapped.
There's also a story titled The Secret Origin of the Duck Avenger, written by a couple of US Disney magazine people. It tries to explain the setup of the PKNA universe... by totally changing the story. It's pretty easy to find back online if you want to read it, and it's pretty short, so it's worth checking out.

After PKNA and PK² ended, but before PKNE was published, a lot of PKNA spinoffs got made by writers who weren't involved with PKNA. The most well-known spinoff is, of course, the complete reboot PK - Pikappa, but there were also some stories by the Dutch publishers and two stories set in a universe where Donald and Uno never met.

The videogame included a comic, establishing its setup. (As a quick side note, the storyboard for the videogame's intro was also released.)
PK - Pikappa was originally going to include a story titled Fahrenheit, and it was to be drawn in a manga-inspired style by Claudio Sciarrone. The story was mostly-lost and shelved. He also remade Mess@gio in Codice (the bonus story from PK #11) in manga style, and it can be read at the end of PK Il Mito #29.
One of the pages from the bonus story of PK #30 was scrapped, according to inducks, but I can't entirely figure out which page it's referring to. If you do know - contact details are at the bottom of the page!
For some reason that is utterly beyond me, the Dutch publishers decided to write three fairly short stories (1, 2, 3) and eleven(!) one-pagers (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11), all printed in the Disney XD magazine and apparently set during PKNA. At the time, only a handful of PKNA issues had been printed, a few years prior, and (other than a reprint of #0/2) it was going to be another 6 years until PKNA would get a proper release.
In 2014, right before PKNE was published, a long-running classic Duck Avenger series called Paperinik Appgrade started printing two 5-part stories of 100 pages each, set in a universe where Donald and Uno never met each other. The first story (PK Universe) involves classic Duck Avenger trying to fight off the Evronians, while the second story (Duck Avenger and the Fangus Machine) follows on from it, with a classic Fangus-just-being-his-usual-self plot.

Paperinik: New Era was released in 2014, and is still ongoing. Despite its long run, it only has about 15 main stories. There are only a few ones that are easy to miss, assuming you kept up with the switch to Fuoriserie:

The fist PKNE story has some extra material - not only is there an alternate start due to it being published in Topolino, but Donald's choice at the end of the first PKNE issue was voted for by the readers two weeks before the story went to print, so there is a two-page alternate ending as well!
There is a collection of 6 10-pagers, set during PKNA, titled PK Tube. Some of them are gag stories, others tie into the plot - regardless, they're worth a read!
For PKNA's 25th anniversary, two stories were printed in Topolino instead of Fuoriserie. They are A Legendary Ordinary Night (Una leggendaria notte qualunque) and Free Zone (Zona franca).

Easily-missed stories!