Any games like this? :D

Fallout 3

I remember Stranded (probably Stranded 2), twas fun, a bit old though... And it's non-Steam.

StarForge might do it for you. It's in Early Access, so it's still being developed.

Minecraft with mods

Skyrim You can buy houses as well with one of the DLC

It's not out yet, but is on Steam Greenlight. Planet Explorers. A open world RPG with some action, with building of structures and so forth in a sci-fi setting.
http://steamcommunity.com/sharedfiles/filedetails/?id=129199308

The other is Kenshi, which just recently got approved from Greenlight. Closer to a RTS in style, but still all the things you are looking for.
http://store.steampowered.com/app/233860

I can't really think off too much beyond that with at least a large size world on top of it.

I can think of a few different games that might fit the bill for your OP, but I think mostly they are in early access/alpha/beta phases etc.
StarForge for sure is, and is very slow in the updating.
There's another game called Planet Explorers that I tried out and find fairly enjoyable, but is also in Alpha.
And then I only briefly checked out the game Windborne, which I think is much closer to release state.

All three of those games are full 3D with a strong emphasis placed on building. Planet Explorers actually has some survival elements to it as well, needing food and drink etc, nasty enemies, etc. Also has quests for the other survivors, and some pseudo RPG mechanics to it...
So I think that would be the best choice for you to check out.

Hum... Starforge maybe?

Oh wait I did forget one. State of Decay has base building. I'm just not sure how advance the base building is and how much control you have over it.

starforge.. I haven't played it personally though

Rust. Never played it, but seem some live streams, looks decent. Also beware Rust may include male genitals. http://playrust.com/

Under the Ocean maybe. I haven't played it though.

wurm online
archeage but its not out yet, but definitely check it out, it looks awesome.

Maybe Mount & Blade, Mount & Blade: Warband and M&B With Fire And Sword(in wfas you can upgrade castles and towns better than in previous 2).

wait for everquest next/everquest landmark
gonna be beast, check trailers and gameplay teasers

Dark Cloud 1 & 2? Not sandbox though.
EDIT: Oh Steam, didnt actually spot that last sentence! Mount & Blade then I guess.

State of Decay?

Windborne, but it's still in pre-alpha. I have tried and it's not too stable (for me anyway) yet but it looks really promising!

They had a big giveaway on Gamepedia not too long ago those keys are gone, but if you click the link, and read the 3rd sticky, they are still handing them out occasionally.

Cube World doesn't have building feature yet, but the game is quite good already.

no one said don't starve

Skyrim's creation kit.

Garry's mod but it don't have very large maps :(
You can modify it with mods so you can make zombie survival etc.

If you don't mind the fact that it is still in alpha: The Dead Linger

7 days to die has all your requirements:
http://www.youtube.com/watch?v=gIYoEO5utUU