For boards I make myself (via blue sheets, etc.), I like CirCAD from Holophase (www.holophase.com). I can generate a schematic and import the schematic components to a PCB sheet and lay them out. Doing things this way radically cuts down on wiring errors as opposed to just drawing a PCB layout.
For boards made by a board house, I just downloaded some proprietary software from ExpressPCB (www.expresspcb.com). With this free software, you can design boards and send directly to ExpressPCB for manufacture at the touch of a button. A quantity of 3 (2.5" x 3.8" each) double sided boards w/plated through vias, no silkscreen nor soldermask can be made for $59. I haven't used this yet, so no comments on quality.
There are lots of other CAD programs out there that have limited functionality (like limit number of parts, no saving, no printing, no gerber output, etc.), but would probably serve a hobbyiest just fine.
i've used WinBoard and it is ok, it has pretty good features like layering, zoning, etc. so you can make fairly complex designs that look very professional. it is a commercial program, license pricing is based on how many pins you want... for a 500 pin license i think it's aroudn $50 or something...
The only problem is that it is a 30 day demo + that it is limited in the number of things you can do before it bombs out. Keep it simple, then it does not bomb out. Save often, so you don't worry too much about bombing.
I haven't used it yet, but when I get some free time, I'll probably play with it. You can download the free version from http://www.cadsoftusa.com They have versions for both Windows and Linux! The free version is limited by the size of board and number of layers. (All info is available on the website) They also have newsgroups on their servers you can read and learn more through.
I use Corel-Photopaint to construct a 1:1 (or 2:1) image of the copper side. I then print the stuff on a laser printer and sent the printed sheets to a dutch company P-S-D which make a positive mask and the pcb. I then receive the pcb AND the mask for future use.
The bottom of the board brings in the +/- supply for op-amps, signal lines, grounding returns, etc. via a card edge connector. The selectable signal, front, rear, left, right, center (all programmable via jumpers) goes to electronic crossovers (programmable via jumpers as to band pass, high pass or low pass). The upper half of the board consists of 2 power amplifiers, less the heat sinks of course. Power for the amps comes in alongside the board via a shielded, twisted pair. This board, along with identical others, is destined for a tri-amplified home theater/audio playback system along with an appropriate speaker system which I am also working on.