I guess the least popular Amigas here at the Underground Arcade office would have to be the poor old A2000s. Both of them have been killed by their clock batteries, and sit in our temporary Amiga graveyard next to a couple of CD32s, some A1200s and an A500. Yet if we can ever afford to get any of them fixed, I know for sure it won't be the A2000s going first, the A1200s and CD32s are far more useful (one of the CD32s has a fully decked SX32 in it).
Still, I do wish I can get those old A2000s up and running again some day, I think it'd be fun to experiment with the wide range of Zorro II cards out there.
It's funny how the A600 was traditionally the least popular Amiga, yet lately with more hardware expansion options available for them, they've become more popular at last, an that's okay with me because they're so cute! My A600 has a USB numeric keypad, mouse, control pad, and can go online. I use it to chat on IRC and MSN, and for online gaming in MUDs.