Well there are so many options these days but here are some good ones:
directpay.irs.gov. This is a free site that let’s you pay with your checking account for free. The only trick is that you have to do it before the deadline. You need 3-5 days beforehand.
pay1040.com. This has a $3 charge for debit card and a 1.87% charge for credit cards. Why would you want to do this? Well first this is instant, so if you are sitting on January 15 (;-), other than mailing a registered and certified envelope (that costs $12), this is your best option to pay with a debit card. Finally, if you have a card that yields more than 1.87% with points, then it makes sense to use the card and get some points. The other reason is hit your spending limits if that is a real issue.
EFTPS. I have actually never gotten this site to work as it has so much security on it, but you need to register, get a pin via mail and then login. It seems more dedicated to businesses.