Julia Scott, CEO and blogger of BargainBabe.com, put loyalty programs from Rite Aid, Walgreens and CVS to the test, to see which came out on top. Scott said that while the three programs are similar, they do have different redemption guidelines that set them apart.

For the most part, loyalty rewards can be used on anything in the store aside from tobacco, dairy, prescriptions, bus passes, postage, immunizations and gift cards. All rewards are spit out of the register at the bottom of your receipt, so it's important to hold onto that to redeem your savings. Certain products at all three drugstores generate instant rewards upon purchasing, Scott said.

"They are good on pretty much anything, and they can be combined with manufacturer and in-store coupons," Scott said. "The rewards are really valuable and you want to incorporate them into your overall money saving strategy."

At Walgreens, the loyalty program is called Register Rewards, and Scott said it is important for shoppers to use their rewards as soon as possible. The program has the shortest expiration period of the three, at two weeks. If you have three separate Register Rewards for different dollar amounts, they must be used on three different items. You cannot combine them to pay for one item, she said.

"The trick is to try and get them as one big value at Walgreens, and redeem them as one thing," Scott said.

Scott said Walgreens' program used to be the one she preferred; however, due to the shorter expiration date she felt more pressure to use it right away. Walgreens also puts out a monthly coupon booklet that customers can pick up in-store, in addition to store coupons that come out in flyers.

At Rite Aid, the +UP Rewards program doesn't interfere with coupons at all, she said. The tiered reward system in wellness+, which is separate from +UP Rewards, offers customers everything from one-time shopping passes worth up to 10% of most purchases to an everyday benefit of up to 20% off the whole store. Points can also be earned toward free health screenings, and members can talk anytime with a pharmacist online or by phone.

"The [Rite Aid] rewards act like gift cards, you can use them very freely," Scott said. "You can use 12 rewards to buy one thing, so you don't have to count everything as much."

CVS' rewards program, Extra Bucks, is the one that Scott prefers above the rest. The program is instant savings, but every quarter customers can earn additional Bucks for every two prescriptions, and shoppers can earn Bucks equal to 2% of their purchases. But shoppers will not receive change if the item purchased costs less than the value of his or her Extra Bucks.

CVS customers can also find extra savings on social media sites.

"A CVS perk is that if you follow them on Facebook and Twitter, you can get extra offers and coupons," Scott said.

Follow Kate Rogers on Twitter at @KateRogersNews