I like military thrillers, for that I like 福井晴敏, I liked 「亡国のイージス」a lot. He tends to have similar conspiracies in his books, but that was a nice example.
I also like mysteries, with detective work involved as well as the crime, so I like quite a few of 宮部みゆき books, among them 「火車」and 「模倣犯」(quite liked the last one, it's 800+ pages though). She writes books set in the modern day AND books set in 江戸時代, you maybe want to start with the modern-day ones.
I like 東野圭吾, particularly I enjoyed 「白夜行」.
Collections of short stories are also good, I like the collections of police mysteries by 横山秀夫。
I very much love the surreal, for that I really enjoy 三崎亜記, he wrote 「となり町戦争」、 「失われた町」 (didn't like that one as much, it starts good but gets bogged down in the middle), and a collection of stories 「バスジャック」which had some good ones. The stories are set in an unnamed world that's Japan, but some other Japan where something is just "off," like SF but just a bit off. It's modern day but in a different era name, there's odd bureaucracy people expect, etc.
I like to go to Amazon and just see what won the literary awards for the year, too. Lately I enjoyed the story collection 「風に舞いあがるビニールシート」by 森絵都.
Oh and I can't forget a GREAT disaster novel that's gotten tons of press too, 「死都日本」by 石黒耀. Basically a giant volcano underneath Kyushu erupts and destroys everything, but it's FULL of science details (got a great following among volcano scholars) AND manages to be a minute-by-minute thriller with lots of narrow escapes and death and lots of descriptions about what it would be like.
Anyway... off the top of my head. I can check the bookshelves when I go home...
p.s. i got permission to repost this on akibare's behalf.