"Games with condom use" is pretty general, and I've played a few that have condoms as gameplay, whether they 'do it well' is up to you.
Imouto! Life ~Monochrome~
You can buy condoms and choose to wear one each time you fuck her. Condoms don't break so each one guarantees a safe cum inside. You're also told which days are safe and which are risky, so you can manage condom use around that, or just pull out every time. There's also an 'after-pill' which stops pregnancy if you take it soon enough. Getting imouto pregnant is game over, and it can be a bad or good ending depending on your stats.
Imouto! Life ~Fantasy~, aka Living with Sister: Monochrome Fantasy
Same as above, except it's a medieval fantasy setting so you don't know which days are safe or risky. Also you can only buy items once every week, so item management plays a bigger role (in Monochrome you can order an item and get it delivered the next day).
Runaway Girl and Me
You can buy condoms, and each condom lets you penetrate her once; you can't fuck her without one. I assume this changes as the game progresses, but I've only played a little bit of this one.
