Most of the transcription tools listed are free. If it looks like the tool primarily captions video, simply export or convert your audio file into a video file. Visit here for more information on file formats, and be sure to also check your host to see which file formats they support.
dotSUB | Free with login
Subtitle Horse | Online subtitle/captions editor
Accessify | Provides a captioning tool
CC for Flash | Captioning integrated into the program
Subtitle Workshop | Free download
MovieCaptioner | Free download
Amara | Free with login