If we consider the purpose of this forum: Usability then it seems that there is some concensus here (at least between you and I bragadocchio).
1. Directed pop-ups to enhance the usability of a site - Good.
2. Note that a new window/pop-up will be introduced - Good.
3. Testing the viability of alternatives to pop-ups - Good.
4. The use of pop-ups for internal links - Bad unless used for point 1.
5. Using pop-ups for adverts/spam - Bad.
The customer is king - if your technical solution sours their experience of the site then you must ask if the solution was the best option. Still firmly entrenched in the 'keep it simple stoopid' principle.
Which brings us onto the the suggestion that a pop-up can be used for online help. OK, but if users need help in filling in a form then could it be that the form is not very usable. Would it not be better to add some words to the form that state 'Enter your URI in this box. If you do not have a URI then leave it blank'. This way the user will not be left wondering what to do and are less likely to up with the message 'you have not filled in the box' when they click on submit.
Remember, users are imaptient when it comes to the internet - if they are not sure or confused they will often not persist (which links nicely to the Worldwide Usability topic:
http://www.cre8asite...p?showtopic=411