Being a NewEnglander born and bred, Fenway is the only one in this category (with the exception of Wrigley). Therefore my top 3 would be BOS, CHI(NL- even though I've never been there), and BAL.
Of the newer ballparks, PacBell Park in SF is the only onbe I've been to and I thought it to be mighty nice (sans the 25-ft. Coca-Cola slide in left field).