Typically hand-made means that the knife started as some sort of metal stock, was heated until it was red hot, then hammered into shape by a person with either a hand-held hammer or some sort of mechanical hammer. Then it is ground on a wheel or belt of some sort, again by hand. The more expensive knives even have hand sharpened and finished edges, as in the last guy that touched it put it to a stone or something to give it a final edge as opposed to just running the edge on a wheel and calling it done.
Machine made knives are typically stamped by a machine from a sheet of stock and finished by an assembly line.
These are generalizations of course, but it should help in answering the question about what makes a hand-made knife.
The handles I am not too sure of. If it is a machine made knife with little human interaction then the handles are likely a cast plastic of some sort. I think a lot of wa style handles are made by another source than the maker that made the knife. I would think that the handles on these knives are hand done with the difference being the level of finish and quality of wood or materials used. Of course machines are used in almost all cases, but they are machines like grinders, sanders, etc. that require a person with some skill to operate.
A couple off the top of my head that I know are hand made (because I have looked at them, lol) are:
Yamashin - http://www.chefknivestogo.com/yamashinknives.html
Goko - http://www.chefknivestogo.com/gokoknives.html
There are many, many more that are hand made on the site, typically those with a japanese name. lol You will also find some knives by American blade smiths as well. The pages usually mention something about a blacksmith or some such which is a good clue that someone made the knife.
I don't know about the Tojiro ITK line, but the DP line is machine made, as are knives by companies like Shun, Global, and Mac. Not to say that these are bad knives, just that there is not a blacksmith involved with beating out the steel into knife shapes as far as I am aware. lol
I am positive there is someone (or quite a few "someones") that can give you a WAY more comprehensive list as to which knives are hand made. I'm still new to Japanese knife makers myself, so while I know how a hand made knife is typically made, I don't know for sure exactly which makers or which lines of their knives are hand made.