I've only had a quick look and sadly I cannot seem to find a list of specific games from older generations that did not include manuals. 

One specific game I know that doesn't have a physical manual is Tales of Symphonia Chronicles for PS3 (NTSC/Collector's Edition & PAL) because I was cataloging my collection and my copy missing a manual seemed odd, and all the sales I looked up were also missing one and the best I got were forum posts of people asking and others confirming yes, that game had no manual.

So it might be the case that users will have to manually report which games never came with physical manuals (or possibly find a list), I'm sure the list of pre-8th generation video games that didn't have manuals is small, likely why there's no comprehensive list, but I'm sure others would like to have those listings updated.

EDIT : Just a small heads up, I noticed the PAL versions of PS4, Xbox One & Switch are still recording "manual only" prices, I can confirm the PAL versions also do not include manuals (unless there's some rare edge cases I'm not aware of) so those would also need to be updated to stop recording "manual only" prices.

I concur with this, if there could be someway on the backend to have listings could not include a manual if the game originally didn't so Price Charting isn't giving those games fake manual prices that would be great. It was rare but happened through previous console generations, like PS3 there's a few but I've heard of a few 90s and even some 80s games that didn't have one, but now it's a lot more common with PS4, Xbox One, Nintendo Switch, PS Vita and even 3DS (which most the time do not have game manuals and instead just generic promotional booklets and safety booklets) and I imagine sadly, this is how physical releases will be 99% of the time, so it's a safe bet PS5, Xbox Series X and any other future systems will be the same.

This feature is great, I'd like to request an update to it though and allow us to specify the currency when entering the original purchase price, as changing the price listings on the site between USD to GBP for example, isn't reflected in the original prices.