As a hand tool almost-purist, my most used tools are:
1/2" chisel
block plane
card scraper (and burnisher for it)
3/4" violin knife
ryoba saw
old Nicholson rasp
half round and knife style needle files
coping saw
jeweler's saw
spokeshave
hand crank drill (get a 2mm brad point bit... useful size for a lot of things in guitar making)
cam clamps (two each of 4" and 8", three 6")
6 or 7" combo square (doubles as a short ruler/straightedge)
36" straightedge graduated to 1/64" (for checking flatness of surfaces and accurate measurement of fret slots and bridge positioning)
and of course, a few grits of sandpaper.
As far as specialty tools go, for fretting you'll at least need a saw to cut appropriate width slots, and flush ground nippers.
A coarse diamond stone is great for leveling frets, as well as sharpening tools and shaping bone nut/saddles. You can skip leveling on your first guitar and just make the action a bit higher, but if you do level then you'll also need a fret crowning file. The offset diamond file from StewMac is excellent, but expensive. Either pay it, or look for an old style file from someone who upgraded
Not worth paying full price for an old style file, IMO.A thickness caliper for plates is nice to have to check evenness and sanity-check that your thickness is in the general vicinity of "normal" (every piece of wood is different, so exact numbers mean nothing). You can make one for cheap using a dial indicator and plywood.
If you're building a steel string, you'll need something to route saddle slots and truss rod slots. I use a dremel with StewMac router base, but a laminate trimmer would be better. You'll also need a bridge pin reamer. StewMac and LMI sell good ones. Grizzly sells bad ones.
For binding channels, I use a gramil and chisel. Tricky and time consuming work, but much cheaper and less space-consuming than a router jig.
For bending, I use a hunk of 3" exhaust pipe from the local muffler shop scrap bin with an electric charcoal starter shoved into it, and run through a dimmer switch.
A lot of the tools you'll need will depend on what construction style you want to do. My style is most similar to that shown in the Cumpiano&Natelson book. Most common seems to be the radius dish+go bar deck+solid outside mould style. Read all you can and decide what's best for you.
