I know pop ups are not good and should be avoided if possible but is that really true that now, whenever i think of using a pop up, i should always be considering other options? Are there any exceptions? And the last question is: what is the default replacement for pop ups?
You can use any javascript based dialog. Look for example at jQuery UI Dialog
The "Web2.0" pop-up might be a lightbox. I hope these are just a passing fad, because they are kind of annoying (a lot like pop-ups).
Banners, like you get at the top of Stack Overflow to tell you about badges, comments, see the FAQ if you're a new user are my favorite. They don't really get in the way and can link to the main content.
It depends on what you are trying to accomplish. Pop-ups are completely acceptable in certain contexts. The aversion to pop-ups arose from having pop-up foisted on users in the form of advertisements. I think that pop-ups are still a valid device in the correct case.
My rule of thumb is to not make any decisions for the user that they can make themselves. This typically includes opening a pop-up since they could right-click and choose "open link in new window" if they so desired.
Do you want to capture of a piece of user input without allowing any further interaction? A modal dialog is your friend.
there are cases where you want to offer a bit of useful info or a quick reference that doesn't necessitate closing off the rest of the web page or navigating to a different location. This could be addressed using some javascript and floating div's but many times a pop-up will do what you want without being obtrusive to a user.
I tend to read resources from the likes of 37 signals and UIE to keep up with the best ways to enhance user experience without alienating a user.