I used to hang out on Batoto/Vatoto occasionally, when that closed down I was recommended MangaDex.
Generally I just use Nyaa though, I think community bandwidth-sharing is just a better model for the internet. There's also an interesting manga zite(s) I use on ZeroNet, the old 0-gallery or newer 1+Gallery (these frontends share the same p2p data model). I've experienced so many sites go down that I'm a bit burned out on investing time in them, although as a lurker I'm really glad other people do, on MangaDex particularly.
Sadly these "permanent" p2p solutions just aren't there yet: they lack a lot of features and are slower than a traditional site. On top of that you need p2p software to access them, this means they'll always have a smaller community. I do hope that's the future though, that when MangaDex inevitably goes down (may it live long beforehand!) there will be a permanent solution to replaced it.