This is a common problem with Gnotella - its file searching routines can be *really* slow. About all you can do to avoid this is either 1) Share fewer files or 2) reduce the number of connections you allow. Basically the more searches it responds to and the more files it must scan, the slower it gets.

This is unfortunate as sharing more files should be a good thing, but I hear the next version will fix this (soon I hope).