My wife and I are trying to have a baby... Its been difficult. She had cysts removed from her ovaries. What are some non-drug ways to up our chances?

Pregnancy difficulty. You need to know when your wife is ovulating in order to increase your chances of pregnancy. There are commercial kits sold at drug stores that allow a woman to determine ovulation. You want to have intercourse within a 72 hour window of ovulation.
Check Ovulation. It requires 4-6 months of unprotected intercouse to conceive for most couples. Your wife can keep a log of her ovulation - best way to do that is by using ovulation kits. And that will let you know the best time period to have intercourse to conceive. Your wife had cysts removed from her ovary. If it was related to polycystic ovarian disease, you need to see ob-gyn for further eval and treatment.