I always have to confront this issue, as I am limited to one backpack on the bank, and one backpack plus a part of a crate and a small hatch in the kayak. Usually I've got 2-3 plano 3500 (or 3600) boxes for hardbaits and terminal tackle, and a bunch of plastics in their original packs inside the backpack.
To choose baits to bring, the first thing I do is make sure I have covered three areas of the water column: topwater, mid-depth, bottom, maybe a few of each. Then I want to make sure I cover different speeds. I want some faster moving baits to swim, buzz, walk, jerk, and some slower baits to fall, hop, drag, twitch, shake, or deadstick; preferably some of each at each area of the water column. For instance, consider this combination of 6 baits: Buzzbait (fast top), Popper (slow top), crankbait (fast mid), wacky-rig senko (slow mid), jig (bottom), texas rig worm (bottom). That might cover the basics. Of course, you'd adjust depending on conditions, type of cover, forage, etc. Maybe bring an alternate or two of each kind. What I don't do is bring an entire box of poppers or entire box of crankbaits, or 7 packs of senkos. One or two of each, three max, maybe different to cover different sizes, shapes or styles.
For color, I choose based on water clarity and light. For clear water and bright days, I want natural colors -- greens, browns, and forage patterns (bluegill, perch, shad, craw, etc.) -- and flashy things that catch the light -- silvers, chromes, and flake patterns. For murky or stained water, or overcast/dark I want darker or bolder colors for contrast and visibility-- purples, blues, reds, golds, chartreuses, firetigers. When in doubt, black is never the wrong color for any condition. I avoid bringing multiple colors of exactly the same bait.