"Chocky" by John Wyndham
"This is How You Lose the Time War" by Amal El-Mohtar and Max Gladstone (a new all-time fave for me)
"The Book of Strange new Things: A Novel" by Michel Faber
"The City and the City" by China Miéville
"The Fifth Science" by Exurb1a
"The Initial Fold" series by Nick Adams
"Peacemaker's Code" by Deepak Malhotra (still not sure why this is not more well-known)
"Eifelheim" by Michael Flynn (a most unusual premise and a gob of seemingly inane stuff to get through at about the 2/3 point, but IMHO worth it)
"Providence" by Max Barry (heart pounding)
"Hench" by Natalie Zina Walschots
"Orange World" by Karen Russell (short stories but many qualify as sci-fi, very memorable to me)
And here are some definitely well-known examples that also stick in my head:
"Infernum" by Jayson Adams
"The Fourth Wing" and "Iron Flame" by Rebecca Yarros (more fantasy than sci-fi, but very well done if you can handle two or three extended and explicit sex scenes)
"Rabbits" by Terry Miles (book includes some hidden hints and puzzles that lead you to things outside the book
"We are Legion (We are Bob)" series by Dennis Taylor
and I wish someone cleverer than me would read Nick Harkaway's "Gnomon" and then explain it to me.