Besides extending the E?
Resume all or some of the A to Brighton Center, Oak Square, Newton Corner, Watertown.
Run down Washington St through the South End and Roxbury, connecting to the Central Subway via the Tremont Street Tunnel. Maybe continue it down Warren and Blue Hill to Mattapan.
Somehow split a line off the B to Harvard (several options - all of which involve tunneling under the Charles to get to Harvard)
Greenway/Charlestown Waterfront trolley.
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Those are the ones frequently discussed with regards to the current Green Line, along with an integrated Urban Ring.
As far as getting the Central Subway and the Riverside line off of LRV and operating the street-cars independently, I'm not sure how you could connect them. The E would be a spur. The B and C would be forced to turn at Kenmore.
But if you really want to speculate, pull out a map of all the major bus routes. Almost all of them used to be street-car lines at one point or another.