Resistance is FEWTEL

"FEWTEL" is an acronym woodworkers use to remind themselves of the order in which they process wood from rough sawn lumber to finished parts.  Following this particular order will result in you handling the wood in the most efficient way, reducing tool setups, and minimizing the amount of time you spend shuffling lumber around the shop.

F: Flatten one FACE of a board.

A power jointer makes quick work of this.  If you're into the hand-tool-only approach, you're going to be using your Jack, Jointer/Try, and Smoothing planes.  I'll let Christopher Scwarz explain how to use each of those tools for this task.

E: Square one EDGE to the face you just flattened.

Again, a power jointer makes quick work of this, but a jointer/try plane doesn't take that much time or effort either.

W: Rip the Board to WIDTH.

Now that you have one square edge and one flat face, you can safely and accurately rip the board to width.  Rip cuts go with the grain, crosscuts go across the grain.  Most people use a table saw to do this.  Some people use a bandsaw, then having to clean up the edge because the bandsaw doesn't cut as smoothly as a table saw.  And some people do it by hand with a handsaw or panel saw.

T: Plane the Board to THICKNESS.

You've got 3 parallel / square surfaces so far.  Now you work on the as yet untouched / rough face of the board.  You can use a power planer which does this very quickly, or you can do it by hand, again with jack, jointer/try, and smoothing planes.

E: Square One END of the Board.

In order to cut the board to final length, you need to be able to measure from a straight edge.  If the end of your board is all crooked, you won't get a reliable measurement.  Squaring up the end before you measure is the way to go.  You can use a radial arm saw, table saw with miter fence, hand saw, or shooting board (or some combination of a few of them).

L: Cut the Board to Final LENGTH.

You've got 5 square/parallel surfaces.  One more to go.  Measure from your squarely cut end, mark the length, and cut precisely.  Make it nice with a shooting board if you want.  

Congratulations!  You just made a rectangular paralellepipedon.

"[...] the word “cuboid” is sometimes used to refer to a shape [...] in which each of the faces is a rectangle (and so each pair of adjacent faces meets in a right angle); this more restrictive type of cuboid is also known as a right cuboid, rectangular box, rectangular hexahedron, right rectangular prism, or rectangular parallelepiped." - Wikipedia

Why I Don't Follow the FEWTEL Method Exactly

I lack confidence, so I tend to leave extra wood at the cost of having to touch the boards more often.  The wood I purchased from Dunham Hardwoods was flattened on 2 faces, and jointed on 1 edge (S3S - Surfaced 3 Sides), so much of this work was already done for me.

After assigning parts to boards I find spots where I can crosscut a board without sacrificing any important parts.  I do this by hand with a crosscut panel saw.  I consider this cutting to rough length.

Then I rip those boards to rough width, leaving a little extra because I'll hand plane them down to final width and I want to leave a little extra in case I screw up.  I use the bandsaw for this and it leaves a ragged cut that needs to be jointed smooth.

I don't have to thickness these, so I just smooth them to remove the planer marks.

And finally, I square one end and cut to final length with my miter saw and shooting board. 

Not that many extra steps, and I feel more comfortable leaving some room for mistakes as I'm still in the learning stages.