If you include Commuter Rail from back in the 1960s and 70s when the MBTA took over for the B&M, there are many stations that were discontinued, or entire lines that were abandoned.
The Central Mass line of the B&M was also a lightly used commuter rail line that ran between North Station and South Sudbury as of 1964. Commuter service ended in 1971, and freight died out around 1980. You can still see much of this line in the towns it served and a few stations remain standing. There is talk that this line will be made into a rail-trail, but since it runs through some very affluent towns, local opposition might leave this corridor untouched.
The other B&M/MBTA Commuter Rail line to be completely abandoned was the Lexington Branch. This line ran from Boston to Bedford until a severe snowstorm in 1977 put it out of service. Since traffic was very light, it was eventually abandoned, and built into the popular Minuteman Bikeway. You can still see stations at Bedford and Lexington as well as various railroad artifacts along the route.
The Woburn Branch was also abandoned in 1981, and believe it or not, it's very hard to find any traces of it today.
As far as stations that are no longer used, here are the ones on the North side that were used when the MBTA first took over, but not today. I'm not sure how much remains of some of these locations, as many of them were probably not much more than a simple platform. I'm sure I'll miss some, so please add any I missed.
Clematis Brook
Beaver Brook
West Action
South Ashburham
Gardner
Mishuwam
Nashua, NH
Merrimack, NH
Manchester, NH
Concord, NH
Shawsheen
Lawrence (old)
Rosemont/495
Methuen
Route 213
Also keep in mind that all of these lines once had many more stations that were discontinued long before the MBTA entered the picture.
Who wants to tackle the South Side?