Light foot and Silence from the Sneak tree carry over, Mage armor and Magic resistance from the Alteration tree carry over other then that there isn't any others that carry over. The Light armor skill tree USED to effect you werewolf but it was changed with one of the patches, BUT all spells carry over if cast before changing so armor spells like Dragons hide will aid your werewolf, cloak spells are another useful spell for werewolves. Potions and food will carry over when consumed before changing as well, some racial abilities like Beserker rage will carry over as well when cast before changing.
Mess around and find out what carries over and what fits your build/play style and become used to having to use hunting tactics as a werewolf and you will become the true monster that werewolves are.
Happy hunting
