I've built a few guitars from scratch and one from a kit. The easiest way of getting into it is to make a body and buy a neck from intornet or from bruce millers or somewhere. The neck is the hardest part to make well and how well it's made determines how well the thing plays. The body is far less important in my opinion.
If you want something simple to start with, make a telecaster. Can't get much easier than that. All you need is a router, a drill, some sort of saw and sandpaper or an electric sander (preferably of the belt variety). You could get away without the need for a router if you choose two pieces of wood approx half the thickness of the entire body thickness and cut out holes for pickups and neck in the top one, then once it's glued to the lower piece, it looks pretty much like its been done with a router. A good thing about this method is that you can hid all your wiring channels very easily by routing or chiseling channels into the inside face of either the top or bottom piece and then they can't be seen from outside the guitar which means you don't need a scratch plate to hide everything.
You can see a few of my guitars here:
PeteBuchan - Photobucket - Video and Image Hosting
The white strat was made from a saga kit and is just used as an electronics experiment these days. It had about 22 different pickup combinations on it at one point. I'd avoid buying saga strat kits.
The diagonal strat thing which you can see me playing was my first body and has a fender neck. Something like that might be easy enough to start with if you can cope with the additional work of the body contours. It was made using the 'two piece' body method (although this is not the traditional 'two piece' method).
The telecaster shown with my ac30 was my second build, again using a neck bought from bruce millers. It's semi hollow (much like one of the other pictures showing the inside of a tele which will soon become my P-90 loaded tele). Sounds awesome - I recommend doing something like that.
The hollow 12 string lezzer was next I think. It's got a through neck and some nice rosewood accent lines. I put 'f-holes' on this one and you can hear the volume difference immediately so I'll be using f-holes on any hollow guitars I make in the future.
The t-bird bass is also through neck, and has LED inlays with a chaser circuit. Avoid making through neck guitars. They are just to be avoided.....at all costs!
I have a few others, but they are pretty much different versions of those.
Pete