This is a really hard question to answer. Many titles probably had an initial run and that was it. If any titles had additional manufacturing runs, it was going to be the early ones that proved popular, as they would have the longest to sell out and need re-printing.
Aside from that...
Keith Courage, obviously. But also Bonk's Adventure, since that was a pack-in. Ninja Spirit was a Duo pack-in for a while, so that probably had been made in larger numbers as well. I doubt it was made to pack-in, but rather made a pack-in because there were extras around. Beyond that, unless someone has manufacturing numbers, it's all guesswork.