It's wrong for your ex's wife to be taking your children to doctor's appointments without your knowledge. You are legally entitled to know about doctor appointments. Still, this is more of your ex's fault than his wife. He is technically supposed to be in charge of his own children while they're in his care, not her, and he's supposed to be actively communicating with you when it comes to the welfare of your children. Even if she takes the initiative and tries to arrange things on her own, it should really be under the authorization and approval of the biological father, and he should be the one held responsible.
As far as school meetings go, I personally believe the presence of your children's stepmother during parent-teacher conferences is more of a good thing than a bad thing, especially if she's the one who helps the children with their school work while they're with their father. She should be in attendance in order to get important information regarding your children's education first-hand, so she can help them while they're in her home. After all, she is a parental figure in their lives as well, even if her role is smaller than yours and your ex. The more support they get from home the better, even if it's coming from your husband's spouse. If this truly does bother you, make sure to make introductions at the beginning of the school year, so the teachers know who you are and who your husband's wife is.
Your husband's wife planning birthday parties during your ex's parent-time is not something you have control over. She should have a right to plan parties while the kids are in her care since she and your ex are partners in their marriage. One thing I tell my stepchildren is that there's one good thing to being children of divorced parents-- they get twice as many birthday parties and twice as many presents at Christmas time than children who live with both parents. Of course, if there are other conflicts, such as inviting the same friends to both birthday parties, then I can see the problem. This means you need to discuss things in advance with your ex-- not his wife. Let your ex know that you plan on having a "friends" party this year, and that perhaps he could plan something else special instead. As hard as it may be, you need to try to communicate with him and avoid planning things with his wife. If that doesn't work, then know that at least your children are having one of the very few advantages of being children in broken homes... they'll have more parties and more presents.
I am assuming the reason why these issues are bothering you so much in the first place is because you feel your role as your children's biological mother is being threatened by this other woman. Be assured that your place is not truly being threatened. She will never be able to replace you. Step-parents are not there to replace biological parents. They're there to fill in gaps when the other parent cannot physically be there with the children. They are supposed to be an addition to the family. Not replacements.
Please keep in mind that your husband's ex probably has her own identity issues, which is why she is so controlling. Being a stepmother myself, I know exactly the kind of emotional stress most stepmothers go through, even the most psychologically sound person. Maybe she feels she should receive more credit than she does, since she devotes so much of her time helping to raise your children. Instead of trying to fight with her, try to understand where she's coming from. She is probably doing her best to make sure your children feel like "normal" children while they're in her care. She probably wants your children to know that they are loved and that she is there to help them if they need her.