SNES probably has the greatest collection of RPG as far as I'm concerned. FF's 2 and 3 (otherwise known as 4 and 6), ChronoTrigger, Lufia 1 + 2, Breath of Fire, Secret of Mana, Illusion of Gaia,Mario RPG etc. Just some really great games that relied on great story telling, as opposed to some of the newer games that hope fancy CSs and massive summons will appease the crowd.
One of my favourite strategy-rpg series of all time is the Shining Force series. They've carried on in different formats but Shining Force 1 and 2 on the Sega Genesis were tons of fun.
And I'd be remiss if I didn't mention Destiny of an Emperor for Nintendo. This little gem was a blast. Over 200 potential party members and the sweet battle option called 'All-Out', which more or less sims the battles for you and saves a lot of time during all those trash mob random encounters.