I have been reading Matthew's Blog for a little while and he just Posted A Guide on what he does to sub raw anime. I have always wondered what the various tools where and how they where used, so this was a very interesting read for me.
If you are lazy and just want links to the various bits of software that he uses:
Subtitle Workshop (for subbing and timing)
Sub Station Alpha (is used for styling the text and this tool isn't in development anymore, but you can do what this tool does in Subtitle Workshop anyway)
VirtualDub (an excellent free video encoder, but the plugin he uses to encode the raw video with the subtitles isn't in development anymore either)