I'm definitely open to other suggestions, but I refuse to do business with Paypal as a result of the company having stolen over $300 from me in the past.
PayPal can be a pain, and I've had issues with the support for PayFlowPro back when it was Verisign.
Authorize.net is the heavy -- they are behind a lot (most?) of the payment processors out there, like Chase/Paymentech. Their API is nasty and their approval process can be cumbersome.
TrustCommerce has a very nice and documented API. For basic subscription charging I think they might be the winner. I am still evaluating their support, sales, fraud protection, etc.
Google checkout is nice but no support for automatic subscriptions.
Amazon FPS is very very nice -- especially if you are accepting payments from overseas and from consumers -- but a lot of people don't like whisking the user off to another site.
If possible I will do an A/B test of TC and Amazon to see if there really is difference in conversion rates, errors, fraud, etc.
Assuming your asking about traditional merchant processing (the latter) I'd recommend CyberSource, combined with your own merchant bank that actually knows you (not one of those "specialized" merchant banks that just handle your credit card processing.
Also, I'd assume that you're integrating the APIs through ActiveMerchant? I'd definitely use that regardless of which reseller/merchant provider you choose.
They have a nice api and their website is easy to use also. I have used authorize.net in the passed and this has been a little bit easier to use.