For me, McToran were the best for nostalgia, compactness, and a simple but attractive design. After that are probably the Voyatoran for their size and variety- though they had no new weapons or colors, and some had mildly awkward designs, I really enjoyed them. They matched my 2001-inspired concept of what a Matoran is better than any others since, with their tininess and whatnot. After them is a three-way tie between Metrutoran, for their versatility, Mahritoran, for their complex build, and Av-Matoran, for their (mostly) bright colors and new masks. They all have points knocked off their enormous size. I think that the Av-Matoran could be favorites of mine if they weren't super-expensive and as tall as the Toa Mata.
In last place are the 2003 Matoran. I hated those guys. They looked like weird, awkward body-builders and somehow managed to remove all the endearing qualities of the McToran. Those bizarre chests...