Apple's iPhone Configuration Utility 2.0, released this week, isn't designed as an end-user troubleshooting tool--it's really meant to help enterprise users create configuration profiles for device deployment--but it provides two functions that can be very useful for troubleshooting.
1. It can uninstall applications directly from the host computer, which can be useful for removing stubborn apps that cannot be deleted directly from the iPhone. Some third-party applications can cause systemic issues, which can be resolved through their removal via a host computer.
2. It allows easy access to the iPhone's console log, which shows application and general system errors, successful or failed attempts to connect to networks, and much more. These logs can prove invaluable for pinpointing otherwise elusive issues.
Additionally, according to Apple:
Configuration profiles are XML files that contain device security policies, VPN configuration information, Wi-Fi settings, APN settings, Exchange account settings, mail settings, and certificates that permit iPhone and iPod Touch to work with your enterprise systems. For instructions on how to use iPhone Configuration Utility, see the iPhone and iPod Touch Enterprise Deployment Guide, available for downloading at http://www.apple.com/support/iphone/enterprise/