Adored by the Network: PUTT. PUTT. SAVES. THE. ZOO. As if it wasn't enough for being marketed up the wazoo when it first came out, Atari seemed like they just couldn't let go of it, not in re-releases nor digital distribution. Nimbus only heightened its adoration; on top of the fact that it was the first one they released, it clearly is their favorite, having more publicity than the others as well as having an interactive book based on it written by them.
Keep Circulating the Tapes: The first two games seem to be falling into this. Somewhat understandable given the way they look now compared to the later games, but they have not seen a re-release since their DOS to Windows ports in 1995.
No Export for You: Putt-Putt Joins the Parade and Putt-Putt Goes to the Moon had very few translations.
The Other Darrin: Clarence and Gert sound different in Goes to the Moon than they do in Joins the Parade.
Pep's Birthday Surprise had quite a few things that didn't make the final cut:
An Apple Orchard mini-game, which would have been accessible from Torvil Tractor's farm and allowed Putt-Putt to continue bringing apples to Mr. Baldininote mentioned in one of the Debug Rooms and in Dummied Out data
Marvin the Marvelous's Confirmation card being separate from the Party Bagnote seen in one of the Debug Rooms
A Decorations area and/or mini-game, which would have been accessible from the interior of the Party Storenote mentioned in one of the Debug Rooms
Another clickpoint animation for the left light at the Fire Station, removed because Leah (Verre?) didn't like itnote mentioned in Dummied Out data
The Party Box being separate from the Party Bagnote seen in one of the Debug Rooms