I only know of one cart ever made for the ST in its original run, and that was a RC Helicopter simulation. It used the cart for the custom RC controller.
The R/C Aerochopper game seems to be a special case. It has software on the card but also needs software on floppy.
As for other cards, there were also two hacker/ripper carts:
Then there was the Atari Diagnostics card. Further the Spectre Apple Mac emulator needed the original Apple ROMs on cart. Then there were a few carts with utilities.
There were various sample cartridges, video digitisers, hand-scanners, real-time clocks and even teletext decoders that used the cartridge port but those did not store the software of the cart. The game B.A.T. had a dongle used for outputting digital sound and was also used as copy protection. But again the software was still on disk.
Then you had also the ROM-disk that used bank-switching to have a higher capacity than 128KB and a whole bunch of eprom chips (I believe even on a 2nd PCB bolted on the main PCB). There was a utility that generated the eprom images from the programs you wanted on the ROM disk. Unfortunately I can't find any info on this on the internet.
Finally there was the Discovery cartridge that had special hardware to copy protected disks.
More info about carts in this thread.