Checkeeper is described as 'works with virtually any pre-printed check stock. Including: Versa Checks, QuickBook checks, Sage checks. It doesn't matter'. There are five alternatives to Checkeeper for Windows and Online / Web-based. The best alternative is Online Check Writer. It's not free, so if you're looking for a free alternative, you could try Printboss. Other great apps like Checkeeper are CheckSoft (Paid), CheckMate (Paid) and CheckStream (Paid).
Save Money! Print your checks on blank check paper available at a fraction of the cost of preprinted checks from retailers like Amazon.com and others. Application allows you to print blank checks on check paper stock. Unlmited prints. Free trial $49.99 to buy.
CheckStream enables customized check design with control over the content, size and shape of every document. It provides the flexibility to add variable messages with complete power over the style and position of fonts, images, and logos on every check.