It's summer and time to put together a reading list. My suggestion is Neal Stephenson's Cryptonomicon. And thanks to dragonwriter for the assist in wording the question correctly.
Neal Stephenson's <i>Cryptonomicon</i> frequently references "Finix" ("Finux"? something like that), an obvious stand-in for Linux. IIRC, Stephenson chose the pseudonym to avoid geek rage if he mis-reported some tiny detail of Linux.
There are, IIRC, a few of the Laundry Files novels - by Charles Stross - that mention Linux, although I'm not sure if you'd say it is featured in a "significant role".
I would recommend Digital Fortress by Dan Brown, I would not say Linux plays a significant role, but the whole cryptography background going on it's really fun and entertaining.