If I have a character with the negative quality infirm (because he is a cripple) and the spell shapechange do you think he would still suffer all the negative effects of infirm while in wolf form?

In my game he would.

Then again he could just use Levitate to get around most of the associated problems.

infirm doesn't really do what the name says at all. it just prevents you from making certain skill checks (unless you buy those skills). if you have a houseruled version of infirm that gives a penalty to physical attributes, for example, shapechanging might fix that. the version presented in the main book would not be corrected by shapechange at all, because the one in the main book doesn't affect physical attributes, it effects skills.

While that is all true, my response was directed more to the fact that Tomothy stated that the Infirm Quality in this specific case stemmed from the character actually being crippled.

It doesn't heal you of your wounds, so I don't see why it would heal you of your long term problems unless it is a form without whatever is crippled.

Chris