Skype by far, is not a cheap alternative to phonecard use...maybe there are other calling services i donno about though..

Skype to landlines/cell phones cost from 0.35 to 0.40 cents/minute depending on where in Nepal you call.
Personally, I haven't ever called out of Ktm using Skype so can't tell you about the quality there but within Ktm, the quality is pretty good compared to the one you get with most phonecards but as you see, it comes at a price.
Besides, since the connection problems are mostly because of the inferior telecom network, you will probably experience a few losses here and there...but it's good while it lasts..

PS: In order to limit risks while using a personal Credit/Debit card, you can always get around using Paypal.