Two different things going on. Offsite links are automatically formatted by tikiwiki to open a new window, and it'll be a fresh window each time. Most browsers intercept the call and display the new window in a new tab instead; if you're getting new free-floating windows, it may be a browser configuration thing.

I wired up the treeTOC to open in a new window, but I tried to set it up to reuse the same window each time. Don't know why it's opening fresh windows each time, but I find it annoying too. In just a few minutes I can end up with dozens of tabs and no clue which one holds what.

But what to do? The operation to create the treeTOC consumes a horrific amount of server resources (one database search for every message to get its replies), and I was hoping to minimize reloads by viewing messages in another window. I'm not sure how to do it better within the limits of HTML.

You've seen in the prototypes how I'm trying to address the issue in Flash. I think displaying the message inline, along with the reply and edit editors, is the Holy Grail. You'd never leave the page, and the whole thing would work more like a classic computer app than a Web app. With that under development, I tend to shy away from investing significant time in fixing the old HTML implementation (which is why I waited until so late in the game before biting the bullet and creating the present treeTOC...only because the Flash UI is still a few weeks away from ready).