*It could offer a PCB fabrication service (outsourced, of course). You pick your PCBs in the counter.
What would be the advantage compared to directly ordering a PCB on the Internet? With the CNC mill one could offer simple PCB production on the go. Although the PCB wouldn't have professional quality they would have the advantage that the customer could get them now. One could even think about providing a simple etching service, too. So customers don't have to mess with chemicals at home. Professional quality should of course be outsourced.
Having empty PCBs of popular open hardware projects in stock (Arduino, OLS, bus pirate, etc.) would be nice. And reprints (maybe only as e-papers?) of the project descriptions.
In general, a big fat catalogue of projects customers can flip through to get some inspiration. Customers can buy copies of the project plans for a small nominal fee (e.g. $1). If they buy the BOM or just 50% of the BOM in the shop they of course get the project plan for free. Kind of a huge bunch of kits, but many more than usual and more flexible - only buy the parts you don't already have.
Another service a real great local electronics store should provide is "calibration". Customers could bring their instruments like multimeters and oscilloscopes and get a quick check against a reference for a small fee. If they leave the instrument in the shop for an hour (warmup), they could get some better comparison with a reference. I would not offer adjustment (too many different procedures).
I like the idea of having the mill on a window and have it making PCBs as an alternative to toner transfer. I think the service shouldn't be expensive, maybe in the $5 range because the boards have no silkscreen. I don't know the details of making PCBs with CNC mills but doing dual-layer boards is going to be hard (nobody is going to manually place vias and solder them in place).
The store could also rent equipment in-store. You bring your project and measure / characterize it with real precision equipment, like Dave's Agilent scope. It also gives you access to tools a small business or a hobbyist cannot afford, pretty much like a hackerspace without being a nerd-club.
Apple offers a similar service in their headquarters. They give you access to a room for a limited time, it's full of different Mac models from different years, each loaded with several versions of Mac OS X. The point is that developers can test their software on these without spending a fortune on hardware. Here it is:
http://developer.apple.com/labs/Having empty PCBs of popular open hardware projects in stock is a good idea. I think a better way to do this is to offer the blank boards and sell the individual parts. For example, I order an Arduino clone designed to be a kit. I already have the AVR, so I ask for everything else. Some guy in the back looks at the parts list and picks all the parts from the cabinets except the AVR. Then he puts everything in an antistatic bag and possibly labels it. The labeling could be automatized with a thermal tag printer and a touchscreen computer with some software that loads the list and allows you to remove and add parts for a particular order and bag. That also makes handling claims easier.
"In general, a big fat catalogue of projects customers can flip through to get some inspiration." This is essential. Oops, I suggested the previous paragraph what you typed after this.
Plans for the kits could be printed on the go. It only takes a good office laser printer that can print very sharp text and schematics and some way to bind manuals.
Calibration comparison is good, but only when customers trust your reference. You could print a non-official calibration sheet.