The "T" is the nickname for the MBTA -- Massachusetts Bay Transit Authority. People usually use it to refer to the subway, but the MBTA also runs buses and Commuter Rail trains as well.

The four lines of the subway (Red, Orange, Blue, and Green) and buses are considered part of the same network, and you can buy a daily or weekly "Link Pass" for unlimited usage of them. This is what you'd use when getting around Boston, Cambridge, etc..

The Commuter Rail trains (indicated in purple on the system maps) are their own network which require you to buy separate tickets: you'd need to take the Commuter Rail to get to Salem and Concord.