Most of the time I do what Tim suggests. There are just a few exceptions -usually if the border is a solid fabric where a seam would be apparent or if the fabric is directional or has motifs that would clearly show a seam unless I matched it like wallpaper (even then I usually just match it like wallpaper! :wink: )
If your fabric is a non-directional print, seams will usually be hidden. The small difference in fabric flexibility is not likely to be a factor if you cut and sew carefully.
Often I will use a diagonal seam when joining border pieces. I can't remember why... I probably had a teacher tell me to do that or read it in a book or something...