They both have good uses. Under the Windows hegemony Arena is easier to use for inputting your matches or setting up positions for analysis.
Not that I want to push winboard on you or anything, if you found something you like then great. The whole point is chess anyway so how can anything be bad. :)
But i just wanted to point out winboard does all that too. You can input games as easy as copy paste from the OS. And with winboard you can manage chess engines pretty darn easily for single matches, as well as manage entire tournaments with them with round robins or gauntlets.
Previously I had used and liked SCID. They have a new fork of this known as SCID vs PC (or SCID vs Mac). These are free and very useful. I gotta revisit this and may vote neither of the above in a couple of weeks.
I took a look at SCID for MAC. Gotta give it props for being a solid, free GUI on the mac when there are so few good ones. If i have one complaint on it is that you can only use FICS as its tellnet connect (If it had to pick one FICS would be my ICS of choice) but it wouldn't be hard to let the user input their own. What if they had a chessclub.com account?