The immediate Sci-fi to come to mind are the Infinity series (Never7, Ever17, Remember11), Zero Escape series (999, Virtue's Last Reward), the Science Adventure series (Chaos;Head, Steins;Gate, Robotics;Notes*), and YU-NO.
I can't vouch for the quality of Never7, C;H, R;N, and YU-NO, but the rest are rather interesting.
If you want more under steampunk, then the Steampunk series (Sekien no Inganock, Shikkoku no Sharnoth, Ourai no Gakhthun**) will be perfect. They all have minigames though; with Sharnoth's considered to be annoyingly hard or nicely immersing with more on the former.
(Can't vouch for Gakhthun's quality.)
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*Untranslated
**Ongoing Translation