Way I understood it, "Trilogy" contains MK 3 Ultimate, whereas "1+2+3" contains the basic MK3, but they're the same thing otherwise?
So, which one should I get? Trilogy is 2$ more expensive, though it's on sale right now, with a 10% discount. (still more expensive than "1+2+3").

Trilogy was a different game from 1996 merging the previous titles in one game and adding things, based in the 3rd Engine and was launched also for Windows 95 machines. The GOG version is bunled with a wrapper to make it compatible with modern computers.

The others are the three independent DOS games running under DOSBOX.

If yu only want one and can afford it Trilogy should be the deal.

If your interest is the price then the original DOS games are also classic experiences.

1+2+3 goes on sale all the time for less than 2 Euros, the triology, being a recent launch wiil probably be a while to see the price as low.
That said, is mind not playing tricks, the Triology is the version to get since it has more units (all of them?) available, including Baraka wich was our favorite, back in the day.
More info on the release thread:
https://www.gog.com/forum/general/play_mortal_kombat_trilogy_and_other_cult_classics_08ccd

Edit: just checked Wikipedia article and as I thought, Brutalities were introduced in the Triology version.

This is correct. MK trilogy is a game, not a collection (confusing, I know) where one could play any of the character versions from MK 1, 2 and 3 on any stages from the same.

Those popular trademarks with a lot of sequels always used to be a confusing mess, indeed.

I can think about the Samurai Showdown thing and I am sure we need a two years master to rationalizing and knowing about every title launched during the years :)

Mortal Kombat 1+2+3 are the DOS versions of Mortal Kombat 1-3. Mortal Kombat Trilogy is a single game that acts as an anthology of the three Mortal Kombat games. It runs on Mortal Kombat 3's engine and has every single character (including the four bosses) and almost all stages from the first three games. Plus stuff like the Aggressor Bar and Brutalities.