If you can find a majority opinion he's written, it's likely to consist heavily of other people's words, albeit not necessarily Scalia's: http://www.nytimes.com/2015/08/28/us/justice-clarence-thomas...
Personally, I found his dissent in Gonzales v. Raich quite interesting and principled: https://www.law.cornell.edu/supct/html/03-1454.ZD1.html
Thomas' Concurrence in McDonald vs. Chicago is also very interesting, as it takes a very different approach to 14th amendment incorporation -- in a relatively unique situation where a judge had to incorporate a BoR amendment that has not been incorporated against the state/local government before -- from the approach that used in nearly all the major civil rights/liberties related decisions over the last 75 years:
https://www.law.cornell.edu/supct/html/08-1521.ZC1.html
Personally, I find the cases where he disagrees with Scalia, or concurs with an Alito/Scalia majority opinion to be quite illuminating.