My riding buddy (and longtime friend) Desmo Steve has an '05 ST3. Maybe he'll see this, and chime in. Until more knowledgeable folks appear, here's what I can tell you:
The '05 was probably the best year for the ST3. The injection system is "pre-Euro3," a lot more tractable than the '06 or '07. I believe that there were some improvements over the '04 and earlier models, too, in the areas of electrics and lighting. I believe that saddlebags were standard on the '05, but were optional on later years. The ST3s has Ohilns suspension, but the standard ST3 is no slouch in the handling department.
The ST3 is the only Ducati that uses the three valve heads. It's water cooled; an advantage as far as I'm concerned. Steve and I have done the valve adjustments ourselves - it's not the dark magic some would have you believe. Valve clearance check intervals were increased on the later models, and I think that the 6K is overly conservative. (Steve tends to drag his out a little longer, with no problems.) Checking the valve clearance is really quick and easy; don't let this be a factor in your decision. Overall, I'd say that maintenance is a little easier than on my ST1300.
Steve's bike has been very reliable. They did replace a coil under warranty, but I don't think that there's been anything else of concern. He rode an Iron Butt SS1000 on it, so I know it's good for distance. The stock seat is surprisingly comfortable. The riding position is "sportier" than my ST1300, but more relaxed than most sportbikes. There are risers available for the handlebars, but they're expensive due to the design.
I think that the ST3 and ST4 models were some of the best looking, and most practical, Ducatis ever made. I don't understand why they ceased production. They accounted for a small percentage of total production, though, and may have cannibalized some of the market for MultiStradas.
Ducati.MS (
http://www.ducati.ms/forums/) is the forum of choice. There's a good support community for Ducatis, and some good aftermarket parts vendors.
I'd say go for the test ride.