nothing on offer whatsoever from 3.1.3, purely a security update from Apple. The only thing is many people have just bought an iphone and a lot of people have had issues that the only way to start is to rebuild on the latest software update - at least this gives those people a chance to get broken again while they wait for 4.0.
With regards to loosing apps, you can download a app that backs up all your apps in a list format and when you download that again after jailbreak it will restore all apps to there former glory.