This is by no means a comprehensive list, just going from memory here....
The former Downsview Station was absolutely built with an eye to allow the later construction of an east-west subway station. There isn't a station box prebuilt and waiting, but utilities were moved, there are kock-out panels in place, and the structure at the north end of the station was built to allow another platform overtop of it. Connections between the two lines would have been made at Wilson Yard, where the tail tracks from the east-west station would have swung north-south and tied in there.
Speaking of Wilson Yard, there are long-standing plans to revamp the access to the south with a grade-separated access, much as at Greenwood Yard. It doesn't seem that the original yard was built with this in mind, but the TTC has called for the allowance of its construction on several of the EAs for the area over the past 20-plus years.
On Yonge, the track alignment was conceived and utilities were moved to allow for the future construction of "mid-block" stations between Eglinton and Lawrence (approximately Blythwood), between Lawrence and York Mills (about Fairlawn), and between Sheppard and Finch. Of those, only one station has since been built, North York Centre.
Sheppard has its own example of this, approximately at Willowdale.
Sheppard-Yonge is more complex than just the built-but-unused platform at the Sheppard Level - there are small sections of side platforms built at the Yonge level, along with knock-out panels to service them. The ultimate goal is to have "Spanish Solutions" at both levels.
You've of course noted the Kipling LRT - there was a matching facility planned at Kennedy and built as well, which was later infamously turned into the SRT platform. If you look around at those platforms, you can see several signs of its original purpose, such as the original low-level platform edge finishes and mounting locations for overhead catenary.
Dan
