There will be as many opinions as people but here is how I organize mine.
I use a small-ish tackle bag by Plano. It holds four of the stow-away boxes (or whatever you call 'em). The boxes have 1. terminal tackle, 2. crankbaits, 3. jigs, jig heads, trailers, etc., 4. panfish lures/baits (just in case). In one side pocket I have a Mepps spinner kit. I also have 5 or 6 bags of soft plastics, Senkos, tubes, Culprits, and whatever else I want to use. There is one larger outside pocket for pliers, scale, and other tools/gear.
I like using the bag because I can substitute the stow-away boxes based on how I'm fishing or what I'm fishing for. It's easier to carry around than a traditional tackle box. I just sling it over my shoulder and I'm off with both hands free to carry rods. Also, it's way more quiet than a hard tackle box, less likely to spook fish when I put it down (I fish from shore mostly).
As for baits/lures, again you'll have differing opinion but...
Must haves: soft plastics, a few crankbaits, jigs, and spinnerbaits. You don't need to break the bank or buy the entire BPS catalog, but a couple of each will do. Also, some decent terminal tackle. Good hooks for plastics are a must.
Here's a quick snapshot of what I use. Obviously it's not everything I own (not even close) but it's what I take on any particular trip.