A lot of the fun stuff that you can do with RavenDB require you to touch the JSON.Net dll. Play with serialization, modifying metadata, etc.
We are using the latest stable of Newtonsoft.Json.dll, and any conflicts that occurs can be solved by asking the other projects to upgrade.
Alternatively, since we consider making the json API visible important, maybe you can talk to the other projects and see if you can make them internalize it.
Last, you can always use binding redirects.