They are both based on the same Sqlite.Net library but the PCL project is a fork which tries to improve on the previous project:
This is a fork of the original sqlite-net library
(https://github.com/praeclarum/sqlite-net), which aims to improve the
code quality by using modern technologies such as PCL (portable class
library).
The project will avoid the use of #if-based conditional code and use
platform-specific code injection instead.
I welcome pull requests, but keep in mind that this library is in
heavy use and all changes must be:
Backwards-compatible (don't change database defaults). Well tested
(please add unit tests).
Both don't support foreign keys.
Performance-wise the PCL project supposed to be better, but that is untested as far as I know.