Does it really matter if those 2 address have different PR ratings? Lets take for example the site that's someone's offering me to advertise. www.domain.com is rated PR3 but domain.com is PR0. So which is which? I just want to make sure that im investing on the right thing.
If it has a PR3 with the www. it means that the domain was marketed that way. The fact that it doesn't have a PR without the www is meaningless provided you don't want to market it in that format. Also, be sure to check the validity of the Page rank here: http://www.seologs.com/pr-check/pagerank.html
The answer depends on your needs and what exactly is your investment. If you are purchasing the site or you are getting link(s) from the site, then you are probably ok. The links from the site would be from whichever the person or bot visited (e.g. with or without the www) pointing to your site. The possibility of the owner creating 2 different versions of the site later with 1) with the www and 2) without is rather remote. Not impossible but unlikely. Having differing PR values on a non-Windows based site is quite normal.
Google considers a website with WWW and a website without WWW as 2 different pages. you should choose one and build all your link accordingly.
you should use your .htaccess file and redirect to the www version. This is called url canonicalization. and it can hurt you...