First, if you really wanted to make popups you could use something like Zuggsoft's MXP. You can create neat, borderline gimicky effects like popups, hyperlinks, and graphics appear in Zugg's clients and a handful of others, but the danger is that like color it is easy to go overboard.

One way to help newbies would be to collect data that correlates self-declared newbies to which helpfiles they look for. Maybe you already do that? The next step would be to ensure that those helpfiles have the RELATED HELPFILES portion of a help entry figured out. If you want to do it right, you could use that data to refer players to helpfiles that aren't directly related, but people tended to access in conjunction with the first helpfile, sort of like on Amazon.

Give flagged newbies an area warning the first time they enter a new area that is over their level or contains mobs aggressive to them. The first time I was in the Galadon cemetary, I remember going from level 10ish mobs to wandering too deep and getting splatted by a juju zombie.

more later. Honey-do list strikes again