The best suggestion I can offer you is to stick to one service.
For example, Marvin (iOS app) and Moon+ reader or Mantano (Android apps) can sync to another copy of the same app via dropbox. Helpful -- not.
The Kindle for PC app will sync annotations, via Amazon's cloud, with Kindle for Android/iOS apps and the hardware Kindles. It offers the best multiplatform sync. And you can use Send-to-Kindle to get non-Amazon-purchased books synced, with annotations. Unfortunately last I heard you cannot download Personal Documents from Whispersync to the PC app.
So -- useless.