The only reason I'm not riding paniers on my fixie is because I don't like how the racks look.. and mess bags are easier to carry around than those puny panier bags with metal hooks on them. I don't carry much, so it's moot, but paniers are a lot nicer for a bigger load. Only problem for me is that my road bike tends to get squirrely with a big load on it.. not sure if it's balance or vertical positioning or what, but it's not fun.

Just my $0.02