That's what my proto-shields look like too. I get the ones from Modern Devices. I've never had much luck bridging the pads so I use bits of colored hook-up wire on the bottom of the board, as well as bent-over component pins. Mostly its a pain in the rear soldering to the chip sockets. The rest of the components are okay.
I color-code connections, too, which helps. Oh, and I stick a stiff wire through the board to make a bus, so I can bring a lot of connections (like ground leads) to the same spot.
It's messy however you do it. Which is why a PCB is so often a better option.