Ditto about the annoyance. Never thought about editing the bookmarklet... I'm going to do that now!

Here's is my slight change to the bookmarklet code. It's not fool proof and and I'll have to see if it actually results in me editing submitted story headlines less often or not. It basically takes the substring of the document title from the start until it finds the first hypen (-) or pipe (|) which are what seems like most sites use when appending the site name.

  javascript:window.location="http://news.ycombinator.com/submitlink?u="+encodeURIComponent(document.location)+"&t="+encodeURIComponent(document.title.substring(0,document.title.search(/[-|]/)).trim())

If you are able to do that you would have my appreciation as the article author! :)