Factorio

Trailer
In this simulation game, the player builds a sprawling factory system. Raw ores are mined, then travel along conveyors to furnaces, which produce metals. Metals are conveyed to assembling machines, which combine them into different intermediate products (eg: copper -> copper wire, iron + copper wire -> electronic circuit). There are many dozens (perhaps hundreds) of intermediate and final products. The player gradually grows a sophisticated and complex factory system to produce them in the right volumes, at the right rates, directed to the right locations. The factory system is built up of primitives: conveyors, robot arms for loading/uploading, assembling machines.
This is akin to VPLs in that you have a system of processes, with inputs and outputs and a notion of conveyance. You have transformations of "data" (metals, products). Playing the game involves design, development, and debugging. As you gain skill, you go through many cycles of design-pattern creation and improvement.

Generominos

A game about building complex geometric primitives using only points, straight lines between points, and circles around points. Intersections create new points.
In other words, a game of Greek geometric algebra — a form of algebra done entirely with the point/line/circle primitives (and extensions to higher dimensions), which is capable of producing sums, differences, exponents, roots, and more.
Rudy Rucker gives a wonderful explanation of this in his book Infinity & The Mind, which is free online. Here's the relevant section: Constructing Reals.
The blog post has some discussion of the design decisions.

A minimalist game where you build a rail transit system. Not related to programming per se, but visually very similar to many patcher-style VPLs. The design language should be of interest to anyone working on patcher VPLs — and besides, it's a good game with good music.

A data science / analysis tool with an interesting drag-and-drop interface. When watching their demo video (warning — it's a pretty large download) I found it fairly confusing and had trouble figuring out what things were, and what dragging them around would do. But it seemed fairly self-consistent, so this is probably just unfamiliarity on my part rather than a design weakness.

An electronic music instrument with a tangible user interface.
Superficially similar to DynamicLand in its tangibility, but focussed on a very narrow use case, and not programmable.
Famously used by Bjork as part of the Volta tour.
Demo Video
Wikipedia
Now available as a mobile app

Wikipedia
Has been used in academia to teach concepts related to programming and chemistry.
This is one of my favourite video games, and a huge inspiration in my own work designing visual programming languages. I highly recommend people buy it (it's cheap), play it (it's fun), and ruminate on it as a possible direction for programming tool design (it comes through with the goods, quickly).