Description: Stripe's take on recurring business models looks really powerful, they can take care of invoicing in the same type of really smart, customer-friendly way they were already doing online payments, you can do wire payments and ACH and still have Stripe notice the payment (it sets up virtual bank accounts for receiving), you can do all types of billing models, etc. and the pricing is great - free for the first million dollars, then 0.4% on top of their payment processing fee. They still don't do quite everything that a provider like Chargebee or Chargify does, but they're getting pretty close.
Description: An invoicing system with everything you really need and not a lot of unwanted features, Cashboard works with Authorize.net or other payment systems to actually let your customers pay. Sending invoices to clients is easy, and it's easy for them to use the site to pay as well, which is critical. We've used it for three years now, no complaints. I like how easy it is to sort and export payment and customer data.
Description: ChargeOver provides awesome subscription billing services for startups, offering both a GUI and a RESTful API. Automatically charge customers on whatever schedule you need, and allow them to pay their way (credit, PayPal, ACH). One-off charges, metered billing, trials, and discounts are all in ChargeOver's wheelhouse. If you can build it, we can bill it, automatically. (Reduced pricing available for early stage startups.)
Description: Chargify streamlines subscription management and recurring billing for thousands of businesses from startup to Fortune 500.
Description: Have a variety of payment systems? Customers both domestic and overseas? Have some legacy cusotmers still paying with older methods? Quaderno pulls your myriad of payment processes together, issues beautiful invoices, and makes tax time easier by putting everything in a single location.
Description: Focused on subscription payments, Recurly manages many payment options and subscriptions, including ACH. It's lightweight but powerful, with a lot of automation potential, and an extremely wide range of offerings.
Description: LessChurn helps your users right before they delete their account by providing them detour options instead, such as extending their trial or applying a coupon. Integrates with Stripe.
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