My wife and I recently rented a place in Portugal. I am a European citizen but my wife is American. We want to stay here for approximately 6 months. For me that is no issue since I am registered in my European home country. What are the rules for my wife since I believe she may only stay here max 3 months ?

If you are legally married married, she can apply for a visa as spouse of EU citizen. Contact the consulate for details.