Like Aw3 said, the only change eMulePlus makes to your system registry is when you register it to handle ed2k links (preferences>general>general). This entry will be overwritten by whichever new eMule software you install, or it will be ignored.
To get rid of eMulePlus from your system:
1. save your downloaded files if they are in the default location in the incoming folder inside the emule folder where eMulePlus was installed. If you have partially downloaded files, save the temp folder as well.
The recommended way is to set up eMulePlus is to set these folders elsewhere in your system, like another partition, even another hard drive, so if you did that, you're fine.
2. delete the emule folder where eMulePlus is installed. Check the properties of the shortcut from where you start eMulePlus to see the path to the folder.
3. delete any shortcuts related to eMulePlus.
Note: in most cases, the other eMule software you install will pick up the partially downloaded files in the temp folder and carry on from there.