As far as I can tell neither is really free. Appfresh's site says it's $14.99 and hasn't been updated since 2013 (says nothing about Yosemite support on the site) - so to me, that's a non-starter. Although MacUpdate Desktop has a free version, it's very sparse in what it does and hits you with ads and emails. To get any real benefit, it costs $20/yr. The MUD app is updated fairly regularly.
That said, I've purchased and used MUD for the last 3 years. I use it for the reasons you state - convenience. It's easier to fire it up and see everything that needs updating at one time rather than discover apps need updating willy-nilly as you open them. $20/yr is about the max I'm willing to pay for that convenience though - if they raise their price, I'd probably opt for the free version.