$5 Sidewinder -
http://shop.store.yahoo.com/surpluscomputers/micsidjoy.html Extremely easy to hack, the pcb has predrilled test holes for the buttons, and the joysticks have big contact points to solder to.
$9.50 Happ Super Joysticks Black
http://www.therealbobroberts.com/ The best joysticks in my opinion because they have a very smooth circular feel, and they're very responsive. Bad 4-way conversion though, but you can get restrictor plates if you want that.
$11.60 Happs horizontal pushbuttons x 8
http://www.therealbobroberts.com/ The best feeling pushbuttons in my opinion, you got 6 for the basic 2x3 layout, and the 2 others for start and select, or coin and 1p start.
$20 wires, solder, female quick disconnects, terminal strips, all stuff you can pick up at radioshack and any automobile store like Shucks.
$30 for the wood, semi-gloss polyurethane, paint, screws, wood glue, assuming you already have all the tools needed. You can pick that up at any hardware store, very easy to find stuff, and its a good idea if you're making a single joystick control panel to make the wood on the top thinner than the rest, or get a router so you can make the joystick higher to the top, so the shaft is nice and long *no pun intended.* If you want the wood to be nice and shiny and scratch resistant, it takes about a month of coating the surface first with primer, then with black paint, sand it, spray again, sand again, repeat bout 4 times, then do the same with polyurethane till its a shiny coat.
And always overcompensate what you think its gonna cost, so I'd say you're gonna have a grand total of $80 for a home made joystick, you could easily go under this if you found cheap wood, went with contact paper, got a good deal on wiring equipment or had it already, etc. If you're only making a single control panel, I wouldn't suggest a full blown I-pac or Keywiz, because they are intended for a 2 player control panel, and all those empty slots to me seems like a waste of money.
-Good Luck