I really wish MNI folks could clarify this a bit but:
MincTool: is a set of commandline tools (very low level minc related IO tools like DICOM2MNC conversion etc).
MincToolKit: is a collectiction/pack of various software pieces (e.g. larger than just commandline tools) to help deal with image processing (including, normalization tools ANT, N3, etc but it ALSO includes MincTool above (e.g. those commandline tools).
MincToolKit v2: is the updated collection of above. Use this. You most likely want to comiple everything all together as MINCLibrary is at the core of everything so for example, just try to compile DCM2MNC won’t work unless you have the MINCLibrary somewhere active.
All this could have been way more simplified. Hopefully you are less confused than before…