We address several common problems with transparent checkpointing and present solutions to these problems, with focus on graphical user interfaces and thread support. We describe two possible ways to retrieve the GUI state from the X-server, by using a proxy for the X-protocol and enhancing the X-server with an extension, and we will present a performance analysis showing that the proposed approach does not imply an overly big performance impact. We will also address checkpointing of threaded applications by mapping of Process IDs (PID) between the application and the Linux kernel.