I've used both OfficeAlly.com and FreeClaims.com.
They allow you to submit claims electronically.
FreeClaims.com isn't truely "free", because they do charge you for certain insurance companies, such as GHI, BCBS, Medicare, etc., although a very, very low fee.
OfficeAlly.com is truely free, and they seem to be better organized. I'm very happy with the services provided by OfficeAlly.com. I do not use their billing software, though. I simply generate a print image file and upload to their website.