my Uno has 4 mounting holes, but the hole next to the reset button is too close to the pin's to be able to use a screw to attach to the stand-off.
Have you considered using Nylon hardware?http://www.usplastic.com/catalog/default.aspx?catid=667&parentcatid=791
I bought a few bags of assorted sizes several years ago and right after I placed my order I found out my local hardware store stocks small nylon hardware.
The problem is the UNO r3 added 2 additional pins (i2c SCA/SDA) over the r2 next to the AREF pin, and those pins are flush with the mounting hole. That means it is impossible to use a normal M3 screw to attach the standoff leg, since the screw head is too big. I imagine you could use a grinder to cut down on one side of a nylon screw head, and screw it from the bottom, or just use a post with no screw to mount it. If you don't have a shield on top, you could just use a longer screw, but many of the shields I've seen now have the two additional connection terminals.
The UNO designers were sort of between a rock and hard place, in that where they put the extra 2 pins is about the only logical place to put it, and if they had moved the stand off hole, it would not have been compatible with earlier designs.