Choosing Configuration Jumpers - Solder bridges, 0-ohm resistors, DIP switches, pin jumpers
For straight-up development boards (for your internal use), I go with a solder jumper or put two back-to-back (3 pads) to make an SPDT switch (here's a footprint I use).  If it's small enough, it's fast to both close and open with a touch of solder or desolder braid.  Using an actual resistor makes it much more difficult to rework with a standard iron.




If this is a product (as in, the Atmel STK500 development board is a product), you should use something like jumpers or DIP switches, because you don't want some dumb user poking around your board with a 1000°F iron.  I'd tend towards DIP switches if you have more options or you are going to put it in an enclosure, otherwise jumpers would be cheaper.

The main question should be "is this something that will be changed as part of normal use?"  If the answer is yes, requiring a soldering iron and skills is inappropriate.  If it's something that an end user might modify 1-5 times (or preferably someone skilled, e.g. a lab tech), a solder jumper might be OK.