Here's a method I use:
latch on edge of first bit in signal
count high data samples for one Manchester bit width (using a clock
prescalar and one clock tick helps if you control data rate)
count same for another tick
subtract first count from second count
CARRY now holds the bit value.

This compensates for small spikes, distortions and so on.

Ed Todd <edtodd@sni.net>
http://www.sni.net/cedardell