Interesting thread - lots of ways to skin a cat, no?
I don't have much to add, but its a subject near and dear, so here goes anyhow...
This is the process I use for furniture or other projects with significant joinery:
1. Buy rough, thick lumber, looking for straight grain (unless you need figure for show).
2. Unless the lumber has been stored locally in conditions similar to your shop, store it for a couple of weeks to let it come to stable moisture content (MC), especially if your project will also use wood already in your shop. You want everything to start at a similar MC.
3. Using a chop saw, hand saw, whatever, lop off an inch from the 'painted' ends so you can see if there are any checks at the end of the board. Repeat as necessary until both ends are check free.
4. Lay out all your finished pieces in chalk on the rough lumber. If grain direction is important, take a handplane and clean the board off so you can see the grain. Draw cut lines allowing for a couple inches extra length around each part. Do not cut anything smaller than a foot (combine several smaller pieces into a single cut if needed).
5. Cut the rough lumber following the cutlines above. If the pieces are more than an inch wider than you need, rough rip them to desired width + 1/2 inch.
6. Evaluate each piece for cupping and grain direction. You will want to run the piece on the jointer with the concave (if there is one) face down, running with the grain. Think of petting a cat, run your hand in the direction of the fur, he purrs, run it against the fur, he bites. Mark an arrow on each piece indicating which way to run it on the jointer. Stack your work near the jointer in order. Have a place to put your jointed pieces nearby.
7. Face joint a piece until it is flat. Put the flat piece against the jointer fence and joint an edge flat and perpendicular to the jointed face (remember grain direction again). Test the two jointed sides for flat and square. MARK THE TWO EDGES NOW TO SHOW THEY ARE DONE. Repeat this process with the remaining pieces.
8. Go to the thickness planer and stack all your work as it should be fed into the planer (grain direction again). The marked face should be facing down. Set the planer to the height of your thickest piece, and run the pieces through. If a piece is smooth, but still extra thick, plane from the jointed face (taking roughly equal amounts of wood from each face makes it more stable). Set each piece aside when it is 1/32 thicker than needed.
9. Stack the wood with stickers to allow air circulation and let it sit for a day or so. You will probably get a couple of pieces not quite square any more. Take these back to the jointer and correct as needed (remember you only have 1/32 of thickness left).
10. Plane everything to final thickness.
11. Rip each piece to final width + 1/32. Joint the sawn face on the jointer in one pass only.
12. Your pieces are still long. Evaluate each piece for the final length cut. This is your opportunity to remove snipe and other shortcomings. Cut each end to ensure squareness.
You are done!
If you are not going to use all the pieces right away, stop before step nine. Do step nine the day you are going to do the joinery.
I know that was long and it probably sounds pretty anal, but in the end it will save time and improve your enjoyment of woodworking. Flat, square wood is easier to fit and produces better results. If you are skeptical, on your next project, ask the lumber yard to mill your boards four square to target thickness. I think you will find the results amazing.
This is just my way, not being critical of the other good methods above! I've used most of them, especially the planer sled, and this is what I have settled on.
