I know for all you folks on MAC you use compressor - but I am a PC guy so here are the tools I have in my arsenal.

Premier CS4 comes with Media Encoder which will allow the encoding of different formats of both  audio and video and works well and allows for batch processing .  Its perfect when you are working in adobe tools and need to export.  However when I need to convert something I use one of 2 tools.  Tmpgenc costs about 100 dollars and allow many different formats in and out and has a ton of options.  Encoding ranges from fast to excruciatingly slow depending on the codec you are using.  At the price its a heck of a bargain.

I also use Sorenson Squeeze which isnt cheap at about $800 dollars although it comes for free with Avid Media Composer.  Its also great and seemingly faster then Tmpgenc (as it should be at 8 times the price) - but if money is an issue Tmpgenc is a great choice and will last you a long long time.