Although I'm giving a presentation on this at IISAC shortly, I know a lot less on these issues than you might think!!
I've never had the time to research/learn all this properly so just fumble my way from one timelapse to the next most of the time.
Like, Alex I use Sony Vegas for the bulk of my timelapse work, including some video editing (cropping/levels/colour etc) which could be done on the JPGs images beforehand if you don't have video editing software.
+++ for free Virtual Dub. this is how i started making my first AVI's but I don't use it so much now.
Another great free application is "Streamclip". If you have your large uncompressed AVIs from Virtual Dub, or in my case FullHD movies from Sony Vegas, StreamClip makes it really easy to resize and convert to different file formats with a number of Codecs included as well. I use H264 for MP4 files or often Apple Photo JPEG for AVI files. If you have Quicktime Pro installed it can render Quicktime MOV files as well.
+++ Fred's suggestion of Photoshop actions (but didn't realise he was so far behind the times
). I have lived off these for years!! For those who have Lightroom, this is an even better option. In either Photoshop or Lightroom, you can also clone out your sensor's hot pixels and then easily apply that same fix every time you capture a new set of JPGs. Unless your sensor has a lot of hot pixels you can easily get away with this rather than dark frames.
For sharing online, I use smugmug:
http://philhart.smugmug.com/Astronomy/Stars-in-Motion
Much better quality/resolution options than YouTube/Vimeo (at least when I last looked). With a pro account you can offer Full HD resolution online.
Now I've given away all my secrets and have nothing left to present at IISAC! I will be doing a presentation on the weather instead!
(only half joking!)
Phil