well i the subject already said the question. thats all :D
As mcwopper said, the size. In basic terms, ATX>Micro ATX>Mini ITX
you can also get larger, I believe most commonly E-ATX and XL-ATX.
essentially, ATX, mATX and ITX will all fit in almost all Full tower/mid tower cases, mATX and ITX will also fit in mATX cases, but only mini ITX will fit in mini ITX cases.
as you would imagine, ATX has more room for features than mATX which has more room for features than M-ITX. This being said, some M-ITX mobos are far better than some regular ATX mobos (sus out the ROG Impact board).
Well as much of a google question as this is.... The main difference between all the boards is the form factor, which basically means their size, with ITX being the smallest, then Micro ATX, ATX and EATX boards being one of the bigger one(there are bigger but thoughs are usually what people buy when building a computer. The other difference would be features and PCI slots, as you could imagine the bigger the board, the more it can usually hold. Though with some of the newer ITX and Micro ATX board they are starting to become really compact with the features which is great. When building a computer, it just depends what you want to do with it and if you plan to take it anywhere.
Size is a "technically" incorrect word, but more or less the proper word.
Form factor, is the technical term. There are a few other out there besides the ones you stated such as BTX but what it comes down to is when computer prices started to come down MB manufacturers were just throwing screw holes around on their boards wherever the heck they wanted and this made building your own system a little tricky.
The first "true" form factor was developed by IBM but to combat this Intel created the ATX form factor in the 90's to streamline things, which is still the most popular for builders. Many of the smaller desktop computers you see around today (Dell, HP etc) use the uATX standard.