I've never heard of a manual transmission car from any major rental agency in North America since the 1980s, with the exception of reading about one Enterprise location in LA based inside a BMW dealer that had stick Mini Coopers -- likely reserved for dealership customers only.
As far as compacts at YYZ, when i have seen them it's typically a Nissan Versa or Ford Fiesta, though they recently acquired a swath of 2012 KIA Rio hatchbacks. No sign of the Fiat 500 at YYZ yet, though I think ERAC calls it an Intermediate.
Sometimes there are no compacts to be found so you'd likely be allowed to take an Intermediate, which usually consists of the following:
Chevy Cruze (only seen a few times)
Dodge Caliber
Ford Focus
Mazda3
Nissan Sentra
Volkswagen Golf 2.5 (seen only once)
They sometimes park Intermediates in the Compact section anyways. Be advised though that the non-aisle sections can be somewhat disorganized. It's not unusual to find small cars parked in SUV spaces and vice versa. This is probably why anything other than a Midsize or Fullsize booking nets you "Counter" service on your res.
IME, you can still go to the lot and choose. If you tell the roving greeters that you're Emerald Club and what you've booked they'll be happy to direct you to your choices. Even with an Exec Selection booking, I'll usually hunt around the other sections to find something interesting like the Golf that one time.