My favorite is satanic verses, by far.
Midnight's children is his most popular work though.
For both books, having even a basic knowledge of Indian history would make the experience much better.
The ground beneath her feet is incredible too. Shame is intense, and if you're feeling thin on South Asian history I'd go with either.
Or if you want to go with European/world history, enchantress of Florence is a good one. Very well reviewed but I personally never read beyond the first thirty pages.
His new book 1001 nights is coming out this Sept. The short excerpt published in new yorker from it was incredible, so that might be a good option too.
East/West is a great short story collection, but has less magic than his novels.
I think Marquez's work is more realistic (and not always evident when he strays into the magical); Murakami sometimes crosses straight into fantasy. If that makes sense at all.
For me 'Kafka on the Shore' contained a bit too many magical events that were then left unexplained and unexplored- but I didn't think it was bad at all.
The other novel I really liked was the 1Q84 trilogy.
Also try Italo Calvino, his short stories are especially good. Calvino writes in many different literary styles, and magical realism is often at the core of his stories. "The Baron In The Trees" was one of the first books I read by him.
For when you have the mental space, a rather interesting / meta Calvino book: If on a Winter's Night a Traveler
I like magical realism though. Any recommendations for other writers?