Well, I can only write about the DVD releases in Spain due to, well, my living there since I was born .
We got so far:
-the 4 Generator Rex volumes as well (comprising the whole first season); I see that according to your info, Kirben, the last ones haven't been released in Germany yet... are you sure about that? I found it weird that we could get them before, I always thought that European countries got basically the same treatment in DVD releases from WB...
-The Secret Saturdays Season 1. First as 2 volumes and then one box set. No news about Season 2 and truth be told, I doubt we'll ever see it, considering that we rarely get more than one season of CN DVDs, with notable exceptions like überpopular shows like Ben10, Clone Wars and the like.
-Hi Hi Puffy AmiYumi Season 1. First as 4 volumes (yes, only 3 episodes per disc except the last one; sigh). Then they were repackaged as 2 box-sets and finally re-repackaged into one single box-set.
-Foster's Home for Imaginary Friends Season 1. Again, first as 4 volumes, then 2 box-sets and finally one. No extras though. I think the US version does have commentaries from characters and the like...
-Batman: The Brave and The Bold:
Season 1 as 6 volumes (4 eps each, except the 2 last ones with 5 episodes each). The 3 first volumes got repackaged as one box-set.
Season 2: in a sudden change of tactics from WB, we got the first 12 episodes into one 2-disc set. Yay! ^^ Considering it costs 12 euros, while the individual volumes cost 9, as you can imagine it's a huge improvement for us local buyers (well, for our pockets, at least).
Season 1 first as 4 individual volumes, then as 2 box-sets and finally a whole season box.
Season 2 to 4: likewise
-Ben 10 Alien Force:
Seasons 1 to 3 (the whole series, I think) following the aforementioned pattern (first individual volumes, later different box-sets)
-Ben 10 Ultimate Alien:
Season 1 Volumes 1 to 4
Oh, and the Ben10 movies too.
-Scooby Doo Mystery Inc (as Scooby Doo Misterios S.A.):
Season 1 was released in a.. particular fashion, similar to the Brave and the Bold DVDs: volumes 1 to 3 contained only 4 episodes each, totalling 12, and then, a box-set named "Season 1 part 2" (alternatively "Volumes 4 and 5") got recently released, comprising the 14 remaining episodes, suddenly all at once. Just like in the Brave and the Bold case, the price difference is abysmal and makes you wonder why in heck didn't they do that from the beginning.
-Star Wars Clone Wars:
-The Tartakovski version was released as 2 volumes... they are out of print now, sadly.
-The new CGI one has been released first as individual volumes and then as season box-sets. 3 seasons so far. Lately a new box-set comprising the 3 seasons has been released too. And Blu-Ray versions too.
-The Powerpuff Girls:
-first an individual volume ("The Powerpuff bluff", translated as "Super farsa").
-then: Season 1 as 2 volumes, then one box-set.
-The Best of the PPG, first as 2 volumes, then one box-set.
-The PPG movie (widescreen format).
-Codename: Kids Next Door (under the name "Código KND"):
Season 1 split into 2 volumes.
Aaand I think that's it. All of them include an English audio track aside from the Spanish dub (and in some cases, like Ben 10 and Star Wars, other languages like French, German, Italian...).
But as you can see, more focus was done on the Ben10 and Star Wars franchises than on anything else CN-related. To this day, I still consider a miracle that they actually bothered to release DVDs of The Secret Saturdays, Foster's and AmiYumi...
Incidentally, I know it's not a CN original, but we got the first 3 seasons of "Johnny Test" as well, the whole released as 4 volumes (each one with 2 discs, with each disc containing around 10 shorts). This release only includes the Spanish dub, though, not the original version (something that it's not too common around here, since we generally get the original audio aside from the dub).