I have used both and very much prefer wooden stand to metal ones. That being said I will throw out the disclaimer that I keep only SW tanks. As such a metal stand + Salt + water ='s train wreck sooner or later as rust becomes and issue and it starts to be difficult to keep it looking nice. So I definitely prefer DIY wood stands as I feel they are more sturdy and durable as opposed to the ones you buy in the store.
Jims use of 4 x 4's and 2 x 4's is a very sound practice. When you consider how much weight a stand is going to have to soundly support and then you consider how much money you have invested in your tank, it cant be over engineered! I have had some 20 gallon Nano reefs that easily had over 2K of money invested in live stock and delicate equipment prone to easy breakage. I pretty much follow the guidelines as far as design goes and build them as per...
http://www.garf.org/tank/buildstand.asp .
Type in all the required numbers and the "calculator" will do all of the other work for you. All you have to do is get the material and cut to size and assemble it as per thier directions which are pretty stupid simple.
Instead of nails I use screws through out and copious amounts of Gorilla Glue on all joints and seams. This creates a rock solid stand that wont come apart without some extremely serious abuse.
One of the stands I built supported a 300 gallon tank and the 140 gallon sump/fuge below with strength to spare. I also built the Canopy that went on it and held 4 x 400 watt Halide retro fit kits and 2 x 160 watt VHO Retrofit kits. Only tools I used was a skill saw and a drill.