For more complex designs, I cut a board using ExpressPCB.
For simple digital or high frequency designs, I use Ivan board. (RF prototyping board from circuit specialists.)
For simple designs, I use standard perf board with holes every 0.1"

<-- Simpler design on perf board.
Note on capacitors: Use the long life caps (>=3000 hrs) even if you have to use a bigger case size in a higher voltage than what the circuit calls for.