Increasing PageRank with Google Webmaster Tools

Some webmasters would not bother if other sites are linking to their sites with or without www prefix, i.e. http://www.domain.com or just http://domain.com. At first glance it looks like there is no difference.

Is it good having your site linked by others in www and non-www format?

Search engines like Google treat these as links to different pages. The real hazard is that you are likely to end up with both versions of the same site spidered, which will create duplicate content conflicts.
Try checking PageRank of your site with and without www. Most probably you'll get different values. Site could have better page rank if inbound links were not spread between www.domain.com and just domain.com.

What can we do to prevent link popularity spreading between www and non-www domain?

The first thing to do is to make a decision on www vs. non-www and follow the same convention consistently for all the links on your site. Use permanent redirects (301) to keep spiders fetching the correct page.
In this way you'll be able to control it on your site. But how to fix inbound links?
You could not control inbound links until few weeks ago. Now situation gets better.
Google provides us with Google Webmaster Tools (formerly known as Google Sitemaps). This tool lets you see how Google crawls and indexes your site and learn about specific problems they are having accessing it. You can see the URL of the page with highest page rank, see PageRank distribution on your site, inform Google which pages are most important to you and how often they change.
One very important feature added recently to Google Webmaster Tools was setting your preferred domain.
In order to set preferred domain add www and non-www site to the list of your sites, verify ownership of both sites (Manage Site Verification link on Diagnostic tab). Then click the site link on the My Sites page and click Preferred Domain from the Diagnostic tab. You can choose from the following:

• Display URLs as http://www.yoursite.com
• Display URLs as http://yoursite.com
• Don't set an association

If you choose don't set an association, Google may treat the www and non-www versions of the domain as references to separate pages. If you choose a version, Google uses that information when crawling links to your site that use either version of the URL. This information is also used to determine how to display URLs for your site in the index.
This new option may help Google to avoid setting different page ranks on www and non-www versions of the same site. This may even increase your site's PageRank since page rank of both site versions now would be passed onto one.