What are some good, cheap and reliable online software payment sites where you have your customers pay through them, like PayPal, but without a reliance on PayPal.

Cardsystems?

I know that Stormpay might be an option or Worldpay.

There's also other payment methods that involve *e-currency* I'd have to look into to it further though for more info since I don't really know much about them.

Examples of E-Currency sites:
E-Gold
Intgold

BMT Micro has always worked well for me.

I bought a peice of software through http://www.shareit.com once.