Ugh! What a pain. I had my circuit prototyped (basically a MAX233 to an RJ-11 socket) on a breadboard, but wanted to turn it into something more "permanent" so I soldered it onto a prototype shield. Not particularly fun trying to solder wires between pins on the underside of the board. Also, it's plugged into my Ethernet shield, but that doesn't work out so well because the ethernet jack is taller than the headers. Argh. I'd swap the order, except that the RJ-11 I have (mounted on a breakout board to begin with) makes the prototype shield even taller than the ethernet one!
I think that's the last time I'll do that. In the future, I'll either stick a mini-breadboard on a shield, or I'll get my own board made.
/rant