Soldering with bus wire on perfboard

One suggestion I can give is to use the thinnest wire possible, and to cut your wires to the exact length you need to route them around your perfboard.

Another clever technique, which I have not personally tried, is to make a "Wiring Pen" as in this instructables

I put together some "Breadboard Hints" at http://lucianifamily.org/getting-it-done/assembly-hints/assembly-hints-index.html#breadboard-hints

Using a combination of clips (Vector T42-1) and pins (Vector K24A) you can put together some neat perfboards. The hints at the site list the supplies and show an example breadboard.

I found this page to be a useful starting point on techniques for prototyping with perfboards:
http://elm-chan.org/docs/wire/wiring_e.html

The techniques used are shown in a video as well:
https://www.youtube.com/watch?v=i5MNLTc7YhY

There is also a company selling some tools, although none of these a strickly necessary and they are a bit pricey:
http://www.roadrunnerelectronics.com/

For instance, this Instructable shows how to create a wiring pen:
http://www.instructables.com/id/Wiring-Pen/