As from the way ed2k works, by downloading 9MB chunks of each file and putting them together as the last one is recieved successfully this means a high portion of fragmentation to your harddisk. To avoid this fragmentation slowing down everything I created a 10GB (5 should be ok) Partition for emule to use as temporary download drive for chunks.The standard folder for downloading these chunks is emule\tempand once a file is finished it is moved to emule\incomingby default.