This subject has been gnawing at me as well for the past month; mind sharing more information about what your application is? My startup revolves around the best option or options as well.
Check-by-mail is being considered as an option (there are a few providers that automate the process).
There's also the technical possibility of using unlinked credits by a credit card processing gateway (user submits credit card # but instead of getting charged the money goes on their card), though so far they (gateway providers) have been very uncooperative about permitting large amounts of the behavior.
Some banks will allow direct ACH's but usually charge a fee per transaction that might make it prohibitive. I wouldn't be surprised if some banks charged less than others.
In any case, my startup is nearing launch and I'd relish the opportunity to meet people trying to solve similar problems.