All right, so my favorites are easy to discern because I've often named characters after them in my own writing.
Boss and the Boys
They're hilarious, especially the Boss. My top pick in the poll. In Secret of Mana Theater (now defunct), it's the Boss who got me started on using the word "mook." Those of you who know me can probably understand my delight at this completely incompetent bumbling fool with grandiose ambitions of world domination and a (two-person!) army of loyal lackeys to lick boots and generally agree with her all the time.
Geshtar
My favorite of the baddies...sort of an incompetent hardass who never gives up. I love it when he takes over the Republic's sandship and one of the crew says "Ack! It's the Empire! Let's surrender!" I always hoped he outlived his final defeat below the Mana Fortress, but probably not.
Neko
Come on...this is like the quintessential RPG character. No one in The Secret of Mana is more "Secret of Mana" than Neko. Neko charges ripoff prices (which I admire) but also has the best gear. And is a cat. A cat!! Whose name means "cat." A CAT!!!
Krissie
Leading the Resistance at only age eighteen, an inspiration for sure! SoM was unusually good at giving female characters meaningful NPC roles.
Popoi
Speaking of which, I always thought the Sprite was female, but I suppose it doesn't really matter. The Sprite is also an imp and a shyster, and ate the ship's ENTIRE supply of food! ^_^
For a game with relatively generic characters and a relatively generic plot and milieu, Secret of Mana sure did have a lot of charm and inspirational value. I consider it dearer to my heart even than Chrono Trigger, because it was my first RPG (if you don't count Zelda's A Link to the Past) and heavily influenced my creative writing over the years. And the soundtrack is just beautiful. It always touched me that the Empire's theme was so pleasant and nice. You can see a lot of my roots in this game!
Poll