Well I never ever had any problem with emule ... there are lots of mods out there with emule and emule doesn't have any spyware whatsoever it's a community based project developed to work on the eDonkey network ... tools include : Fake-checking, File Rating/Flagging, Commenting, intergrated IRC client, Friend Slots ( You can make some peers your friends and give them priority over others if you've got a fil they want/need), You can even send a message/chat to a person who's got the file you need, may also give you priority over other peers... lots more tools ..emule is the bombdiggy!!
Well as for protection ... basics : AVG + ZoneAlarm and for added emule protection : Protowall and Blocklist Manager ( you'll be surprised where some packets come and go!!!) these two block packets from enetering your pc and going to places you don't want to go like RIAA.