While services like previously mentioned KeyRingThing will automate the process of condensing all your loyalty cards, they aren't perfect. If you want to fully customize your mega loyalty card, DIY web site Instructables shows us how to make your own.
Apps like previously mentioned Key Ring on Android and services like KeyRingThing are great, but provide complications—some scanners have trouble scanning phone screens, and having all your barcodes bunched together causes a lot of hassle for cashiers. Furthermore, a lot of services like KeyRingThing don't recognize certain companies, so if you have a lot more obscure cards, it might be harder for a cashier to differentiate between your Wizards of the Coast bar code and your Student ID bar code.
Instead of dealing with all that, Instructables shows us that you have the most control when you do it the old-fashioned way: scan your loyalty cards into your computer and use a photo editor to cut, paste, and spread out those bar codes along your mega loyalty card. You can add in store logos yourself so you know which is which, and you can spread them out enough so that scanning the card doesn't trigger three different bar codes (folding the rest of the card over before handing it to the cashier also helps). If KeyRingThing or Key Ring aren't quite working for you, this old school method is another great option. Hit the link to read the full instructions.
Bonus Card Barcode Hack [Instructables]