Cissyn wrote a post on how "taiji is a pain in the knee" (NOTE: I would've commented directly on his blog but wanted to test if trackback/pingbacks/linkbacks work with the blogger service). I just wanted to add my own thoughts to his great observations.
In addition to the "knee point same direction as toe" thoughts, I also do the "knee does not go beyond the instep". Some ppl used to teach the knee to toe alignment but to me that is wrong and makes it quite painful on my knees.
This kind of relateds to Cissyn's thoughts on song kua, b/c in order to get into a low stance and not let the knees go beyond the instep, you need to have a relaxed kua otherwise it is not possible to do without breaking this alignment.
Another thing I've noted is that for me, it's harder to keep the knees pointing the same way as toes in chen but not so in yang. I personally think it has a lot to do with how the 60/40 horse stance is commonly used in the chen form whereas that's translated to a standard bow stance in the yang set.
The funny thing about the side horse stance is in general the application results in the energy being focused "behind" due to the application of the arm opening, etc , whereas in yang, I feel a lot of the apps are done in such a way where the energy is being focused in front of you. In this regard, I think a lot of the chen apps emphasize the usage of the shoulder/back with a "bump" kind of energy whereas in yang and a lot of other sets, the opponent is generally kept in front. Perhaps it has something to do with the context of the development of the styles.. chen is more rural fighting whereas yang was more emphasis of 1-1 in small confined spaces, etc..???