I did have some thoughts on the matter the other day
https://gbatemp.net/threads/setting-about-making-models-for-prices-for-old-games.591553/
Though short version
Games people like
Games of historical relevance
Games the speedrun or competition set want.
Games collectors want because having a complete set/gotta catch em all.
Whatever quality/rarity/desirability the serious money set are dealing in, and this brings in misprints, first batch, rare batch, owned by someone notable, signed, ridiculous quality concerns (if the box slicer in the factory was in need of a sharpen that day then watch those zeros tumble off).
This is all further compounded by
Rarity. This can include in a given region (PAL at once providing some stupidly rare stuff, and also being looked down upon for a lot) and English language copies are also a factor here; big in Japan but unknown but still available outside it, Japanese copies of western stuff can be a thing too (FPS is not popular in Japan owing to the whole motion sickness thing but there are still some).
If it was a "hidden gem" to begin with then yeah probably not many out there. I reckon you can probably predict hidden gems too; might not be mainstream, indeed definitionally it probably can't be, but there will be enough buzz if you know where to look (Deadly Premonition was probably my first time I really met this for me -- I did the release post and wondered why it was not getting any traction, 2 weeks later we have a sleeper hit and since then... yeah. Though at the same time I am on record as really liking Escape Dead Island, and maintain that one, so I am probably not a great one to ask here).
The complete collector set also seem to struggle with various kids games too.
Lawsuits to recall things, or recalls in general. Depends how many got out as well, and the nature of the recall too (well loved game that saw some licensing rights issue, all the way to the bank, boring game that saw some distasteful issue, possibly see something like "the guy game", harder).
Later rereleases on the same console (grey label being the US preferred term) tend to drag it down for "serious" collectors for some reason, though later rereleases with a bunch of extra content tends to be "tell me more".
It might be harder to shift if you are selling it but it seems there are those that like wasting space on limited editions and tat that comes with them.
Was sold later in the system lifetime, better yet after the next system was out and all the kids were skipping things there. Or if you prefer go look at the pricier/harder to come by versions of those for any system and the release date relative to the successor console.
Was sold exclusively at one shop, better yet an oddball one (see various things sold in Blockbuster in the US, especially the N64).
Was a limited run on physical media. A more modern thing as it was more recently that such things became a serious component of sales. At the same time see what happened to Silent Hill P.T.
Was only available as a prize for a contest or other rewards system (see various Japanese club Nintendo exclusives) rather than shops.
Was only available as a pack in game which was different to baseline -- see Zelda-Metroid on the gamecube, or the emulated versions of N64 Zeldas on the gamecube.
Console it was on was a bit of a failure but has since gone on to be recognised as something somewhat special.
Nintendo probably warrants it own consideration in this; for as long as I have been following games their second hand prices for first party/owned dev even during the system lifetime have been kept fairly high-- I knew enough to wait for some months even when younger and stupid but did Zelda Oracles titles come down in price that much? Nope still £20 a pop when the GBA was already well established.
Likewise RPGs tend to be higher in this if they are at least vaguely playable where nobody wants sports games, give or take a few really oddball sports games for the complete collection set (usually also on Nintendo or rare in a given region -- nobody likes American football, baseball, basketball or nascar in Europe so those few times someone smokes enough crack to think releasing a title like that in Europe is a good plan, never mind for a Nintendo console, then I am sure the future game collectors/those handful that do like the sports mentioned and shoved then in an attic thank them). Even more so if they are part of a series that kicks off but more on that next. I will also add shmups to the list there as some can get to some quite dizzying heights.
Games a dev (be it company or game director that is otherwise known by name) that later went on to do great things for. I often note Demon's Souls/Dark Souls is not the first attempt at such a thing from those devs; see prices of king's field vs what they were before the later games became monster hits/genre defining. Similarly Fire Emblem was a Japanese series that saw a few characters in Smash Brothers, it blew up for reasons that I have never been able to fathom and now watch the prices of the earlier efforts rise. This is probably the harder one here for where I can make a model of the former lot (
https://towardsdatascience.com/predicting-hit-video-games-with-ml-1341bd9b86b0 is not that but similar idea) and as mentioned above there is probably scope for a sleeper hit detector then any dev can seemingly hit a groove and make something spectacular. For instance see The Witcher; EA, Ubisoft, MS, Nintendo, Epic, Sony, Square Enix... all have many or at least notable failed open world RPGs to their name, nobody expected a bunch of early-mid 2000s Polish nobodies (Poland had some tech but were not Hungary or anything, nobody really notable for mods, hackers... meh compared to elsewhere,...) to do what they did with this and yet here we are. Equally even if I can see talent then publisher shenanigans are always an option; how many otherwise amazing studios are the grim reapers of EA, Sony and Ubisoft now responsible for gutting?
I am not entirely sure what effect piracy, emulation and rereleases play in this. At once it can be something, and it is also possibly less than some would estimate.