I've been using my N900 for a while, but i never found an answer to this:
Do we have some sort of an app or a script that will allow us to connect to a certain Wifi SSID as soon as it is in range?

There are only 2 wifi connections i use, one at home and one at the uni.

Note that i know that if i enable 'Connect Automatically' it will do so, but at my uni there are multiple connection at each loaction but i can only access one, so it tries the first one on the list and fails.

My guess is that it would be a big battery drain, as it would need to check the availability of the signal at some interval like every 60 seconds.

It would be nice: When you get into range at work, you'd get the SIP connection to your office extension, etc.

Well, i wouldnt mind it to check every 10 minutes.
Also, if you use the 'Automatic Connection' it will waste more battery on trying to connect to protected networks and such.

You could install a widget called ConnectNow. (info)
After installing it is possible to add it more than once on your screen, it's very customizable with a different icon and even their own name, so you can have one for home and one for Work the uni in your case.

I have similar issue. When I am at home and say I launched some website, then it will connect my home wifi without wifi-selectin prompt. But when I am at university then a pop up with wifi-selection pops up. Is there any way that I can connect the university wifi automatically without me having to select it from the list?

Automatic Connection would be better with an option to connect only to whitelisted networks.