What are the most popular crypto currencies after Bitcoin?
If an online store accepts another crypto-currency appart from Bitcoin, you can be sure 90% of the time it'll be Litecoin (most accept just Bitcoin as of now). It's the one that has the 2nd biggest market capitalization and market depth as well. As to what could be the 3rd most popular, that's difficult.

"Popularity" is difficult to measure directly, but you can use value in fiat as a proxy. Right now, several crypto-coins are valuable about 1 US dollar or more: just go to cryptsy or to coinwarzand check the market prices (given in bitcoins). Given current prices of bitcoin in USD anything more valuable than one milli-bitcoin is worth aprox. a dollar, a lot of coins are worth more.

Another proxy you can take is how frequently you see ads of people asking for donations or offering their services in exchange of that currency - that way, you'll see humble dogecoin being asked/offered a lot, where as protoshares/quarks are almost never asked for in spite of their value. Other coins worth more than a dollar (like prime, name or PPC) would take the lead here based on this metric.