For my scrappys, I like to pick one fabric that I use throughout the quilt to tie everything together, like for the sashings, or maybe background fabric. Otherwise, anything goes. I just toss my scraps into a paper bag and use whatever I pull out. 30's next to CWs next to batiks--my only "rule" is to not use the same color next to itself. Sometimes even I think it looks "wrong" as I am stitching individual pieces, but I am almost always happy with the look of the finished product.
However, I recently read a blog article by a scrap quilter who sorts her scraps into two bins. One bin is full of fabrics that go best with whites, the other is fabrics that go better with creams. Fabrics that could go either way are tossed into whatever bin has less scraps in it. She swore that this made her scrap quilts blend nicely.