I have used WoWMatrix for a few weeks now and I'm fairly impressed. I had some questions which I sent via their website's feedback form and received a very detailed and courteous response. The developers seem to be doing their best to include new addons in supported list and to keep the most recent versions available.

It's probably best to manually manage your addons if you have only a few or if you aren't yet familiar with their installation and use. But once you know the basics and have started to collect a substantial number of mods, a utility like this becomes very handy.