With shut down and prosecution of Liberty Reserve; authorities in US have clearly declared war on virtual and crypto currencies like bitcoin, litecoin and PPcoin.
Here is a presentation on understanding crypto currencies like bitcoin.
Most of the e-commerce carts like Opencart, Magento, Prestashop have bitcoin payment plugins which will allow a merchant to accept bitcoin or litecoin as payment through payment gateway providers like bitpay.com.
However to accept or not to accept crypto currencies as payments is a matter of judgment. As the things stand crypto currencies sit between gray-zone of legal and illegal.