A combination of rattlecans, hand painting, and Sharpies. You can accomplish quite a bit with those and stencils, netting, 1/8" to 1/2" masking tape. I still use rattle cans for primer and base layers especially on large baits.
For some small details and touch ups, I have done a quick rattle can spray into a plastic cup to make a little pool of spray paint. Then, I use a small paint brush from Walmart to hand paint with the paint from a spray can. (30 for $2 in the crafts section). This can come in handy when you get a blemish from removing tape, a bug landing on wet spray paint, or if you drop a bait mid paint job and only get a couple of paint chips. Sometimes a screw up is savable with out starting over.