This is definitely a topic of hot conversation. There is one unfortunate truth: as a user, you can easily do one thing every time you want to open a link in a new window (control-left mouse, right mouse and select, or Apple-click on a Mac). However, if a link forces you to open a new window, there is no way to have it open in the current one.
That's pretty interesting to me.
We had a fairly animated discussion about this on our conference call last night, and there will be more discussion around it. However, a number of systems (including the latest vBulletin) are moving away from this "standard" and towards the standard that we see on most other sites (Wikipedia, Google results pages, and so on). There are still exceptions (as I noted above).
So, the discussion isn't over, yet, but there are also a few emerging standards that may make this decision for us. I'm looking into them now.