I saw a special episode or something of Wizards of Waverly Place where Alex got upset and said "I wish you and dad never met!" to her mom but then she regretted it after the wish came true and her parents didn't know who the kids were. I never saw the end of it but I'd like to find out which episode this was so that I can hopefully find it again.
As Bellatrix says in the comments, this is Wizards of Waverly Place: The Movie. It premiered on the Disney Channel in 2009, so it's pretty fair to call it a special episode of the show. Here are the relevant plot details, up to the point you remember:
The Russo family, Alex, Justin, Max, and their parents Jerry and Theresa are preparing for a vacation to the Caribbean. [...] Once in the Caribbean, the family meets a boy working at the hotel that Alex instantly develops a crush on. [...]
Later, after Alex was about to use a spell on her mother to convince her to let Alex hang out with the boy from the hotel, she gets caught, leading up to a heated confrontation with Theresa. Theresa tells Alex she is grounded for two months, which means she is forbidden to use magic and go out on dates or parties, As a result of this Alex, in a fit of rage, wishes that her parents had never met. The smuggled full-wizard wand and spell book, which Alex was holding at the time, grants her wish. As a result, Jerry and Theresa do not remember Justin, Alex, Max, and they don't know each other.