Here are two good (and of course free) options for manipulating audio files.
dBpowerAMP lets you rip CDs, convert files, and record audio. It supports MP3, MP4, M4a, WMA, OGG, AAC, APE, FLAC, Apple Lossless, and more. This app integrates with Windows, so you can simply right-click on a file to convert it. Get it here: www.dbpoweramp.com
CDex is a CD-ripping and file-conversion app for the extremely picky. It includes many different encoders, including LAME MP3, Fraunhofer MP3, MP2, APE, OGG, WMA, WAV, VQF, and FAAC. It also has jitter correction for error-free CD ripping and works with the CDDB database. Get it here: http://sourceforge.net/projects/cdexos