Super here means "on/based on" someone else's tune, as in the (English) title of Mozart's Twelve Variations on "Ah vous dirai-je, Maman" (known as "Twinkle, Twinkle" in English) for piano. In whatever language they are written (English, Latin, Italian, etc.), the different prepositions used indicate that the composer has based the composition on a musical kernel, usually a theme or melody, in someone else's work. So had he been writing in English, Bach might have named the piece Trio [based] on [the 1524 Lutheran chorale] "Nun komm der Heiden Heiland." There is nothing special about the fact that your examples are pieces for (solo) organ; the principle of using [genre name] + "on" + [a title] is generally applicable to any composition that borrows in this way. Sometimes the composer of the borrowed theme is named instead of the title of the piece it comes from. For example, Brahms wrote Variations on a Theme by Haydn for orchestra.
If you write a piece like variations on your own theme, you can simply leave this fact out of the title (in which case it will be assumed you wrote the theme too), or you can expressly state it. Elgar's "Enigma Variations," Op. 36 for orchestra is actually titled Variations on an Original Theme, and Brahms wrote a similarly titled set for piano. This practice probably started when it was common for one composer to write a set based on another composer's melody or a folk tune popular at the time. It's proper to acknowledge this rather than give the impression you are taking credit for the inspirational idea itself. An example is Chopin's early Op. 2, a set of Variations on "Là ci darem la mano", (a popular duet from Mozart's opera Don Giovanni) for piano and orchestra. Displaying the title of a well-known piece could also be a way of doing a little advertising and cashing in on an earworm people were whistling and humming, or a hymn they knew from church.
The theme for these types of works can also be a person's name. There are several works based on the motif B-A-C-H (H is the German letter for B natural; they use B for our B flat). See this Wiki article for a list of these composition. Schumann wrote Variations on the name "Abegg" for piano. (The big limitation here, of course, is that only the first seven or eight letters have corresponding notes.)
In works (especially variations) based on a theme, it's common practice to present the theme at the very beginning of the piece and in a fairly unadorned way, so that the "original" or starting material is immediately clear to the listeners. This lets them "fix" it mentally and subsequently pick it out as the variations become more elaborate and a lot is going on and also to appreciate the sometimes ingenious ways the theme is treated. Composers like building on a catchy tune or one that is inherently "malleable" as way of showing off their compositional prowess: "Hey word! Look what I can do!"
If you need a short-hand name, I would call pieces like those in your question by their respective genre: a Trio, a Fantasy (or Fantasia), Variations, or Trio on a Theme/Hymn, etc.. And while your examples may be great pieces, by using super in the titles, rest assured that Bach is neither congratulating himself nor supersizing his pieces :-)