Have You thought about using wing bands with RFID?
http://www.roxan.co.uk/index.php/news/6/58/WonderBand-poultry-chick-wing-tag.html
There are also bar code wing bands
http://www.nationalband.com/wingbands.htm
http://www.nationalband.com/WingBandingDirections.mov
Last but not least there are...