There is an unbelievable amount of potential in Minecraft that is completely untapped. It's really an amazing environment and I'm surprised it hasn't spawned "sandbox games" as a completely separate and significant genre, especially since a big reason Minecraft remains "untapped" is Notch's reticence to open the platform up and push the game forward.
Just thought I'd mention CraftStudio (http://craftstud.io/), the multiplayer game-making platform I'm working on. You could say it's a Minecraft-style engine but you get to make your own models, paint your own map blocks and (soon) write your own game rules (so you'll be able to make any kind of games, not just first person stuff).
It is steadily becoming a lot more open - Jeb's the lead developer now and a big focus has been put on adding mod support. They've hired the guys behind Bukkit (a popular third-party mod manager for servers) to help with that, I believe.
Clones have also started to appear but it's still small indie companies making them, meaning it'll take time before many are at the same level as Minecraft.
However, the bigger companies do seem to be paying attention (an EA bigwig spoke about Minecraft in a Gamasutra piece the other day [1], though he was saying fairly obvious things), so it'll be interesting to see what the genre's like in 5-10 years' time.
Have a look at Spout[0]. Its an open source server that generalizes the minecraft concept. They are actually supporting 'minecraft' as a plugin called vanilla which communicates with the stock minecraft client. They also have an improved client which is currently a modded minecraft client but I believe the eventual plan it rewrite the client from scratch also.
I'm surprised it hasn't spawned "sandbox games"
as a completely separate and significant genre
Maybe you haven't noticed, but "minecraft-like" is a a burgeoning young genre - every week I see a new one on the /r/gamedev subreddit or tigsource forums.
And there are already a dozen or so commercially successful ones on steam and XBLIG.
