Just going through the download page (http://www.adventuregamestudio.co.uk/AGS.aspx)
The bug tracker link on the right sidebar on the download page goes to the old one and should be updated: ( links to http://www.adventuregamestudio.co.uk/BugTracker.aspx)
Also, the wiki link there is to the old location, not the current one (although it auto-forwards). The Beginners FAQ links to the old wiki site, but the auto-forward takes you just to the wiki front page.
Many of the main site forum links need to change yabb to forums
The .NET framework download link is broken and gives a microsoft not found page
It's less than easy to update these things unfortunately, as the site compiles to ASPX rather than being easily editable. CJ said he'd give me the source at some point, but hasn't got around to it yet. I'll prod him again. Thanks for making the list though!