Lining up the colours
This livejournal thread explains how to make colour changes in variegated yarn line up when worked in crochet. It does need to be a yarn in which the changes repeat regularly.
First you need to do some experimentation. Chain "lots", then find out where the point at which you are in the colours next repeats, and mark it with a slipknot or something. Now work straight until you reach your marker. Count the number of stitches you have done. Now if you make something in the round that is this number of stitches - or a multiple of it - around, you should be able to get the colours to line up nicely.
Handling colour boundaries
Avoiding colour pooling
Especially with handpainted yarns, the colours on the knitted or crocheted fabric can "pool" giving clumps of particular colours. Some people like this, others want to avoid it.
Apparently daisy stitch can be good for avoiding pooling (seen on Queerjoe's blog comments)
Working alternate rows from two skeins or balls at once can help, too - if you only have one ball then you can try pulling one end from the centre of the ball and one end from the outside to mimic the effect of having two balls. You can either work across and back, change yarn, work across and back, change yarn, etc, or you can use a circular needle to cast on, work across with ball A, push the stitches back across the needle, work across with ball B, work back with ball A, push stitches back across, work back with ball B - this avoids having both balls of yarn travelling up one side. (Seen on the knitted=lace list, originally on Knit U.)