There's definitely something to be said for confidence in your baits. My go-to baits for panfish are 2 1/4" triple tail grubs in floro orange, chartreuse, or white; these colors get used almost regardless of conditions and catch fish. For bass (and pike) I'm confident in 7" ribbontails in pumpkin/chartreuse, pumpkin/orange, and watermelon/red. Tubes in watermelon/candy or watermelon/red. Frogs in any color, there doesn't seem to be any preference by the fish. Again, all of these baits produce for me in any condition/water clarity.
Now that I'm making my own baits, it's fun to experiment and move outside my comfort zone with colors. Experimentation can help you find new confidence colors. Junebug is producing well for me. tomato (what I call tomato, it was me playing around w/ floro orange and red scrap and it came out very close to the pics of tomato colorant) has been pretty good too. These colors have been more dependent on conditions though.
Experimenting w/ having something unique is another great benefit of making your own. For brown tones, I've always liked motor oil color baits, but it's not as widely available as pumpkin seed for instance. When I was buying power worms, pumpkin/chartreuse was my go to color with pumpkin/orange being a close 2nd. Recently when buying colorant in a brown shade, I went with motor oil instead of pumpkin. It's a similar but slightly different color and I'm able to make baits that might not be on shelves. I've also found a small amount (1/16th of a teaspoon or so) of green hilite does a lot for the motor oil colorant. So I have 7" ribbontail worms in motor oil/green hilites w/ a floro orange/gold hilite tail. What I'm making is producing at least as well as the baits I was buying before and I have something very similar, but decidedly different.
Another benefit to making your own is getting ahead of the curve. People on here have talked about Tomato being a hot color in TX recently. In WI, it hasn't exactly taken store shelves by storm however. So I've mixed up something close to give it a try here and results are promising so far. How many people are using that color here I can't say, but I would guess that it's not many. I'm using a color fish maybe haven't seen yet. Bass on Winnebago seemed to like it.
Ok, so short answer time: Colorants - If you can afford all of them, get 'em. But if you're like me and broke, get the colors that will produce well for you as well as some basics that will allow you to experiment and mix up new colors. IE red+blue=purple. Glitter - same as above. I highly recommend holo silver. Hilites - all of 'em. They're affordable enough. UV blast when it comes out will be added to my arsenal. Probably glows as well if they're affordable like the hilites. I won't use them as much, but they'll be fun to play with.