Protyping and Avoiding non Functional Rat's Nests.

Do you have any advice on making stuff solid and stay functional?
It seems that I get rat nest that are non functional when I get semi complex,
and it seems that the sanguino lacks some perks of the standard arduino.
It's be a frustrating experience having it work with a bread board then transferring it over.
(wires slowly breaking, and the like)
I was thinking about purchasing some connectors like these,
and having my sanguino plug into some female headers that are attacked to a strip board.
http://www.seeedstudio.com/depot/20-pin-dual-female-splittable-jumper-wire-300mm-p-629.html
I was thinking I could silicone them in so I can remove them if I want but it would take some effort.
They'd be used for all the input and outputs, as I will have almost all of my sanguino pings used.
Currently I am using stranded wire and a perf(not a strip) board,
I've gotten so frustrated it's been months since I've touched my sanguino to finish my project.
I'd really appreciate some suggestions on what I can do to get some decent prototyping done.

Use strip board and solder it all together. Then use header connectors to plug in your arduino clone.
It is as simple as that. For more complex wiring you could consider using the Vero wiring system.

Thank you for the input, I'll do just that.