I'd get a pack of multi-colored electrical tape. I think the come red, white, blue, green and yellow. Also, get a roll of basic black.
Use two bands to mark the cables on the receiver side. One for the R/L channels, the second for position.
Now, while you have several pairs of speaker cables, all but the center has a right and left. I'd use red for right, white for left.
Mark all the rights with red tape, left with white. That's one band, the channel band.
Now, for the other band, you simply assign one color to the speaker positions: Yellow for surround, green for rear surround, blue for height, etc, etc... The center could simply be left unmarked.
IF you reall want to get cute, you could use the position band to join the R/L wires together to keep the mess back there a little less messy.
Of course, you get to choose what colors for what, but you get the idea.