Having recently made the journey from breadboard to proto board to PCB, perhaps some of these suggestions will help.
First, it is cheap and easy to add a "bare arduino" from parts - 1 chip, 2-3 caps, a crystal, and a resistor if you want a reset button.
(see art364 / Standalone Arduino)
For my project, I combined this on a proto board with the rest of my project. You can program the chip in your Arduino and move it to the board, or use serial.
Since my project was battery powered, I added a 3v-5v switcher from Sparkfun. (Obviously, there are other options.)
Later, I wanted to explore making a PCB, so I bit the bullet and learned Eagle. (There is a Mac version, I believe.) For me, it was frustrating at first, then it clicked, and it was a lot of fun.) I combined the switcher and "bare arduino" on one PCB and made a daughter board for the other stuff. I used Sparkfun's PCB service - slow and cheep.
The point is, that I'm glad I did the proto board first. Like doing a breadboard before a proto, it helped me make a better PCB. One is as good as their options, so you can stop with the proto board if you decide not to go forward.
Perhaps you asked for the time, and I told you how to build a clock. 
So in summary, I'm suggesting to start with #3 and play your option on #4.
John