I will primarily address Pesach, as it is both the most pressing and the most complicated of the holidays in this circumstance.
As mentioned by others, there is no possible exemption for sukkos, since his free half is obligated to be outside and his enslaved half prefers it outside. He must be careful, however, to eat any food he has killed that evening while sitting in the sukkah.
Most fortunate is Tu Ba'av, which occurs right after a period of required abstention from meat eating. לא היו ימים טובים לישראל כחמישה עשר באב - a great day indeed!
The other yomim tovim represent no peril, as they occur at other times of the month.
Since the person in question is simultaneously half-wolf and half-man at the point of transformation, we may point to another halachic half-man in the middle of a transformation - A chatzi-eved/chatzi-ben chorin. As half free, he has an obligation to observe all the mitzvos of bal yira'eh and chametz, but eating the korban pesach is a special exception.
Chazal say (Pesachim 88) that an eved with two masters may not eat from the Korban Pesach from either one. This is because each half is makpid on his ownership of the slave, and this precludes the other half from being yotzei with the other's korban (rashi and tosfos, ibid.) This is extended to one who is only a chatzi eved - the portion owned by the master prevents the freeman from bringing his own korban.
Now, a person subject to lycanthropy is enslaved to his inner animal nature (Rav Jekyll - which is actually a corruption of Yechezkel), and since an animal is not considered to have das, we cannot arrange with the animal to release him as an eved into a status of a full freeman. This would imply that the werewolf is in fact pattur, and cannot even eat the pesach lechatchillah, during his transformation.
However, since he is a completely free man at the moment of the chiyuv of bringing the korban, he still must go to Yirushalayim on the 14th to have it brought. Additionally, we must be choshesh for the shittah that the korban pesach may be eaten until amud hashachar! If a werewolf finds himself released back into human form due to clouds covering the moon or any other method before amud hashachar, then he must eat at least a kezayis of the korban without a bracha (Safek lehakel).
As always, special care must be taken that, in his enthusiasm, he not eat it raw.