do you mean the color to join the blocks to each other or the color to quilt the top where it will show?
for attaching the blocks i use whatever leftovers i have from other projects that are anywhere near the same color family. for the quilting that shows i try to match the color to the color most used in the quilt top, or variegated in that family. sometimes that means changing the threads (ugh!) for different sections. i try to avoid that like the plague!
whatever you choose for attaching blocks don't worry about it. you're the only one who knows what goes on inside of the sandwich. and us. and we won't tell.