Blueprints - Unreal Engine Visual Scripting (Free & Open Source & Commercial)
Links: http://blueprintue.com/ (Pastebin for Blueprints)
Blender Game Engine - Logic Editor (Free & Open Source)
Amazon Lumberyard (CryEngine) - Flow Graph System (Free with Full Source & Commercial)
Scratch (Free & Open Source)
Similar Tools: Stencyl (Free & Commercial)
Gdevelop (Free & Open Source)
Similar Tools: Construct 2 (Free & Commercial)
Note: Basically, there are two most popular types of visual programming as scripting system in game editors - node & wire based and block based. My personal favorite is block based, more specifically, GDevelop-style. The reason is the presentation of logic in block based visual programming is "linear". Node & wire based visual programming is very flexible, but as the presentation can be non-linear ("messy"), it usually has low readability (just think the "wires" as the notorious keyword "goto"). Block based is more similar to line by line text-based structured programming, and it is easier to structure and organize, and hence usually have better readability. Scratch and blocky are too similar to text-based programming and almost have no advantages over text-based programming, so I think most programmers would not bother using them. GDevelop gives a better example of block type - the event driven, condition & action approach is very intuitive and convenient.
Goo Create (Free & Commercial)
Goo Create open source online WebGL game editor has a state machine visual programming system.