I had a minor hiccup upgrading to the 3.1 version.
This was because I had been using NewNewsWire Lite version. When I tried to launch NetNewsWire 3.1, it failed (crash report details below).
Update from the comments: Brent is on the case and has posted a new build to fix this first-run issue. See his comment below for more information and the link. Thanks for the quick response Brent!
If you encounter the same problem, this is what worked for me: Move the ~Library/Preferences/com.ranchero.NetNewsWire.plist file to the desktop. After doing this, NetNewsWire should launch without issue and the preferences file will be recreated. If this works, you can trash the old file that was moved to the desktop.
Process: NetNewsWire 
Version: 3.1 (1200)
Code Type: X86 (Native)
Parent Process: launchd 
Date/Time: 2008-01-09 19:21:31.431 -0500
OS Version: Mac OS X 10.5.1 (9B18)
Report Version: 6
Exception Type: EXC_BREAKPOINT (SIGTRAP)
Exception Codes: 0x0000000000000002, 0x0000000000000000
Crashed Thread: 0
Application Specific Information:
*** Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '*** -[NSCFString timeIntervalSinceReferenceDate]: unrecognized selector sent to instance 0x515990'