I've been using Procoder for encoding since 2005 and I wouldn't change for anything, Procoder 3 is very stable, (unlike Procoder 2).
It can do multiple output formats simultaneously, it's fairly fast and it watermarks

I've done batches of 75 videos at a time without a hitch, left it chugging along for days.
The downside is no FLV, I use Sorenson Squeeze for that.
Vegas can only output 1 format at a time, some content I handle needs 5 output formats, 3 wmv, 1 mpg and an mp4 or mov, it would take all day to do that in vegas.