I personally did not encounter any malware issues. If you're unsure, just download the portable version. I was won over by the multi-threading and available 64-bit portable platform. Extensive encoding options including lame are also a big plus. The interface is streamlined and intuitive even without the extra skins, and recently added CD ripping really completes the package. Unfortunately, starting with version 0.9.4, the Win(x64) downloads ultimately launch a 32-bit process. This seems to coincide with the appearance of the CD ripper. Not sure what's going on there, but I'm confident it will be corrected.
There is Nothing wrong with installer When installing pay strict attention to install. You do have options to skip and not install of snad.do. Note: Those who were complaining about adware were simply not reading or paying attention to what they were clicking.