I interpret this line as very specifically intended to silence Caroline Bingley. I don't think he is being misogynistic, because he would find manipulative behavior equally repulsive in men (perhaps something to address in later chapters), but I do not believe he is joking. If he is, it is dessicated, Sahara-dry wit. He is telling CB that he is aware of her attempts to "catch" him and he is not impressed (by her and/or her methods, take your pick). By casting this as a general statement he avoids insulting her personally, or creating bad feeling among his friends. But CB understands him well enough, because we are told Miss Bingley was not so entirely satisfied with this reply as to continue the subject.

Darcy's statement that "I cannot boast of knowing more than half a dozen [women]... that are really accomplished" I likewise take at face value (am I too literal?) I think Darcy is being straightforward: he does expect a great deal from women. High expectations is the opposite of misogyny. Darcy has had much experience with women throwing themselves, or being thrown by their mothers, in his way (CB is the generic example), who are introduced as 'highly accomplished.' Like us modern day consumers faced with TV advertising, he has become skeptical of these claims.

IMO "A lady's imagination" and "With great energy" are examples of his wit. Even if he is sincere in believing these statements I don't think they qualify as misogyny.