I believe that there are some problems with the "violinist" and "people-seed" analogies used by Thomson, because the picture she paints does not fully capture the situation of a woman faced with an unwanted pregnancy:

1. the violinist in the story has no relationship to the unwilling donor at all: they've never had anything to do with one another until now, and it's only by chance that the two individuals share a common blood type. This isn't the case with pregnancy, where the mother is (albeit unwittingly in some cases) directly responsible for the foetus finding itself in the situation it does. Perhaps we should consider whether it would make a difference if the violinist's kidney failure was a consequence of the other person shooting him (abeit unwittingly) in the back while engaging in the sport of target practice.
2. Thomson's hospital director says to the unfortunate patient "to unplug you would be to kill him", which carries the implication that the death is an unintended, but forseen side effect of the unplugging, and so might be seen as appealing to the Doctrine of Double Effect. This isn't quite the same as the choice faced by a pregnant woman though: I think a more realistic way to put this would be "before unplugging him we have to kill him". And while it may not make a moral difference, it might be added that the method of killing is not always particularly "clean"
3. Unlike cases of violinist and "people-seed", there is a unique relationship between a mother and her unborn child. Our society does recognize this and there are laws which protect this relationship. For example, after a divorce where the father is given custody, the mother will be granted access rights; when a child is adopted it has a legal right to find the identity of its natural mother. Balanced against these rights we should expect there to be some degree of responsibility, which Thomson's thought-experiments completely ignore.

Another issue of concern is that running through the essay is an implication that a woman bases her decision to abort on the problems associated with pregnancy per se. In fact, for many women the issue is not an "unwanted pregnancy" but an "unwanted child": the concerns are chiefly about how they will cope with the responsibility of being a mother and bringing up a child. Thomson may say that the right of the mother to choose the fate of her foetus exists regardless of the motivation for her choices, but I think that once this right is granted, we make it slightly less difficult for women in this situation to choose abortion, when there may be other options (e.g. adoption) that would address the real concern (unwanted child).