I've done it unbagged (twice), but mainly bagged. I've never brewed the same beer and tried a different approach, so I really can't say scientifically it makes a difference. However, it always (yes, two times) seems when I throw them in without a bag I get better hop flavor (better utilization?).
I may go back to doing it unbagged. The clarity of the beers with the hops just tossed in has been on par with those where I've bagged them, so it makes no difference. Actually, the clearest beer I've made to date I just tossed the hops in... Just don't suck them up when racking, etc. and you'll be fine.