The WiX v3.9 release candidate was released last week. Bob, who is driving the v3.x releases, has a few words about the release candidate. I wanted to reiterate what Bob said. Download the release candidate, build your product with it. If something that used to work no longer works, please file a bug.
Update 2014-07-08: A few people asked about a change log of the WiX v3.9 changes. Yo, Taylor, Imma gonna provide you those links but before I do, please, test out WiX v3.9 as it is. WiX v3.9 (like all WiX v3.x releases) are designed to be backwards compatible. That means you can drop it in, recompile the world and everything is expected to come out as good or better.
Please, drop WiX v3.9 in and verify everything continues to work regardless of the features and changes.