Hate to say this the OS, the hardware, the software were not what made the Amiga so popular initially. Having games on floppy disk as opposed to cartridge is what sold more A500's than anything else and made the Amiga the games platform of choice. Cartridge-based consoles were very difficult to pirate at the time, and that meant lots of school boys ended up getting an Amiga 500 where they could get lots of games for free, and swap with their mates at school.
X-copy 2 (bonggggg!)
Hey, I was 14 and earned £4 a week on my paper round, and It's not like I had rich parents who could afford £50-a-game...
My top 3 would be:
1) ARexx (already said, but what a powerful tool.)
2) Unlike the PC of that era, which would become unbootable if you even thought about playing with the boot configuration files, the Amiga almost invited you to.
3) For me, back in ~1990, showing it to my Dad for the first time doing graphics, audio and Word Processing (Kindwords) and seeing him realise that it kicked the pants off the £2000+ PC he'd got for work - although that did have Aldus Pagemaker, which was pretty cool.