When I was teaching in Philadelphia and working 30-45 minutes away from where I lived, I regularly used the citi’s program, TransitChek, in order to save money on my commute. Once every month a certain amount of money (a number I chose) was deducted from my paycheck before taxes were removed and designated towards a TransPass or other train tickets in the city. This (annoyingly) came in the form of physical checks which I had to submit directly to a ticket agent at one of three stations in the city. I am very happy to hear that they have since upgraded their system and you can do it with a debit card they now provide.
The program in New York City, Wage Works, works the same way (and, in fact, TransitChek is provided by WageWorks nowadays). Money is deducted from my paycheck and put onto a debit card. Since it is pre-tax dollars, it means any percentage that might be taken away is instead usable, saving me roughly 40% of the money I would normally use for public transit anyway. It is so easy to use: just put your debit card into the Metrocard machines instead of a credit card and – voila – you use your money.
It is a wonderful system that helps millions of commuters nationwide and I wanted to give it its due here. If you currently work in a major corporation or organization, chances are you have access to it. If you do not currently, check out their website to see if your employer will join.