One the most intriguing aspects of guitar building I've enjoyed learning about, is the various ways luthiers have come up with to attach the neck to the body. The ones in my small collection have these variations:
1) Neck-thru-Body
The "neck" goes straight from the head stock to the butt, and the "body" is comprised of wings that are added afterwards. When constructed of 5 or more layers of woods, it creates an incredibly stable and rigid neck, while still allowing for a truss rod for minor adjustments. My Thunderbird Bass is built this way, and ESP Guitars builds a lot of models in this way.
2) Dovetail Set Neck
Where a dove tail neck base is used to attach it into a mortise-and-tenon type of joint in the body, and usually glued ... most Gibsons are done this way, as is my Epiphone Les Paul and my Takamine 12-string.
3) Bolt-on-Neck
I don't own a Fender, but most of them are built with a separate neck attached to the body of the guitar by 3, 4 or sometimes 5 bolts. It's a quicker / easier method, so often appears on more budget conscious guitars, without really compromising them in any way.
4) Reverse Shoe Set Neck
My old Norman ST30 is similar to a set neck, except that there is no "shoe" visible on the outside where it joins the body. Instead, the shoe is inside the guitar, making it a bit of an oddity. They're not using this method anymore (don't know why) but it's very stable. I bought it in 1978, and it's still perfectly straight and holds tune very well.
5) Spanish Heel
This is an older European way of doing it, where the side pieces of the guitar's body are inserted into slots in the butt of the neck, so that it becomes a fully integrated unit when complete. The result is increased sustain, and lots of dynamic overtone in the voice of the guitar. My Cordoba is built this way, and it has a very unique voice with the 5ths and 7ths quietly ringing in harmony to every note.
This is where the art of lutherie meets the art of music ... a truly beautiful marriage!
