free version of eagle is enough for most hobby projects...
but I don't think making PCB's for everything is a great idea just for simple prototyping as a beginner, I have a feeling you'll find it to be a lot more difficult than using perfboard (or dot-board as you called it)... and to make changes, you either have to hack up traces on your board, or make a new board. With perfboard you can just desolder some wires and fix things easily. making PCB's isn't incredibly hard, but it can be quite time-consuming, which is why I only make a PCB for a circuit after I have it fully working on a breadboard, so I know i'm not wasting my time.