Tune-wise, blue tunes alter your robot's basic stats (dem gamma tunes actually lower your overall stats...*shivers*). Red tunes (weapon tunes) change the performance of their respective tuned weapons. Yellow tunes (ex-tunes) are the same as most basic blue tunes, except they also improve your bot's HP with no extra cost to yoyr robot's capacity (but getting the materials for them...ugh...)
As for boost run color tiers, I used the chart from http://www.cosmicbreakfanforum.com/t7429-boost-run-short-boost-etc-etc-charts
Highest to lowest: pink, red, orange, yellow, green, blue, indigo, violet, gray, brown, tan...
Lots of people aim for yellow-tier boost run, since almost all non-boost running characters run at green-tier speed at their fastest, and they throw the rest of their points into HP and either STR and/or TEC for more damage. The economy boost run core tune makes this better by making running eat up less boost, but it doesn't have any effect on the tier color (distance = speed * time; tier = speed, eco BR adds extra running time; overall result is that you go farther, but only because you ran for a longer amount of time, not because you got faster).