Im not sure if Im asking the right place, but basically Im looking for advice on the best way to:
Record Audio through a microphone on a website and Upload the audio
You can also use FLVAR which is a Flash based audio recorder that runs in the browser.
As mentioned by Konrad, It uses a media server like Wowza, FMIS or Red5.
It supports the 2 audio codecs present in Flash Player for encoding: Nelly Moser ASAO and Speex.
You can use ffmpeg and FLVAR's APIs to convert the resulting .flv file to .mp3.