There are games where you can customize your character, and NPCs may react to your penis size.
Love & Sex: Second Base has a small penis option. Women will say something about it the first you have sex with them, and that's the extent of it. The only other affect on gameplay is that reduces the ogodds of pregnancy. NPCs may say something like "That thing will never please me" if you choose a small penis in
Lilith's Throne. (You can choose to be trans in that game, as well.) You can also customize your character to have a small penis or be trans in
Degrees of Lewdity, and NPCs will react to it to some extent. There's little to no SPH content in any game that I've played where you can choose to have a small penis.
Taco has made some femdom games where the protagonist has a small penis, those being
Second Class and
Slave U. Those are specifically femdom games, so SPH is present, but most of the content is ball busting, feminizing, pegging, using the MC as a toilet, etc. These are part of the "magic women" genre, where women are all magic casters and men aren't, so they've created a matriarchal society and use magic to subjugate men. You can opt out of some types of content, but when you ask for femdom, you're going to get it. It can be a bit much if you're looking for something more vanilla or realistic.
I wanted a realistic game. I modded a game that has no magic, and I made the women respond to the MC's penis in a realistic way. In the real world, women probably won't scream "holy shit" when they see a micropenis, but the reactions are within the realm of possibility. The mod doesn't require too much suspension of disbelief.
There aren't a lot of games that have SPH at all, and most of those that do either tack it on, or go all the way to the extreme of femdom. I became aware of the dearth of good SPH games while searching this site and finding threads like
Games with SPH/Premature Ejaculation and
Looking for games that focus on SPH/NTR and started working on this mod. I see that someone has since compiled a "comprehensive list" at
SPH - Comprensive List and Discussion.
There are also very few games with good trans content.
Fetish Locator has a trans character, as does
Gates Motel.