I use the very old and dead-simple Protel tools, Traxedit or Easytrax for layouts when possible. Though there are some other free or shareware programs out there that will do, I just like these because of how dumb they are. The newer Protel tools (very expensive!) for example, won't place a pad for you unless it is in some complex component library you basically have to get from them, and are so complex that unless all you do is lay out boards all day every day, you'll never get facile with them. The advantage of the dumb version is that for it, a 16 pin dip is a 16 pin dip -- it doesn't have some obsessive schematic capture insisting that you tell it the part number, than asking for money sent to the mothership-corporation to allow you to place the darn thing. The old stuff will eat or put out netlists, however, which is useful. If you type in a netlist, you can then have it show the connections as straight lines between the components after you place them, then re-place and rotate them to make the fewest lines cross before placing the real tracks. Handy. Easytrax and Traxedit are dos-only but do run fine in any dos emulator -- like dosemu in linux. They have a very mnemonic set of commands, and key shortcuts galore (all the function keys plus either shift, alt, or ctrl) but what I do is just use the first letters of the commands in the menu structure. So if the command is going to be "file, save, yes" to confirm the save, the shortcut is fsy. I printed a cheat sheet to lay over the function keys, but that's too much fishing to find the magic key when "pc" means "place->component" and so on.
I will try to find a way to get a copy of the tools I use up here so you can download it and use it, if I get any requests. Both will go straight to a laser or inkget printer transparency, with some nice options, so you can use the readily obtainable positive photoresist pre-sensitized boards from Marlin P. Jones and others. They will, with some hassle, also make gerber plots for sending off to APCircuits or other board houses. We find that the transparencies are a little imperfect in how black the black is (and for the UV types of boards, red works better), so the exposure time has to be found for your system experimentally for best results. We do that here by using a strip of aluminum foil on a strip of scrap board, initially covering all but a little bit of the board, then pulled back one increment about every 30 seconds or so while under the lamp -- the lowest exposure that develops easily is the one to use for best results. This depends a lot on your light source, so I can't give a number for other than my setup, for which it's about 4 minutes under a pretty bright 250w mercury vapor lamp (streetlamp with outer phosphor envelope broken off so the UV can come out). The developer for these is simply a dilute lye solution -- they sell a concentrated, fairly impure version that you dilute, but you can make a better performing one at home with plain old lye (make it saturated) and then diluting it as recommended in the board instructions. You can make it a little stronger for under exposed boards too, but if you overexpose them, you'd better watch closely while developing and get them out of the developer before you lose all your tracks or get pinholes. Sometimes you can fix a gap with a sharpie (the stinky ones resist most etchants), but that's pushing your luck a bit, since the solvent also dissolves the resist that was there, and no way it looks nice once done. Note that lye solution will become sodium carbonate solution after some air exposure...so keep it bottled up and don't mix a lot more than you'll soon be needing.
The way to see if you've developed your board correctly is to use some Ferric Chloride (ugh) on a paper towel, as it will instantly corrode and change color the exposed copper parts. For etching, you can use that messy stuff (permanent stains on all it touches -- even pyrex) or some other, tamer etchant. To tell the truth, there's not much that will do this job that you want to have get on you -- ammonioum persulphate works at boiling temperatures with a mercury activator -- also ugh, but at least you can see through it while etching. We keep this kind of thing in old 2 liter pop bottles between uses.
Note that if you buy solid ferric chloride someplace and do your own mixing -- first, do it soon after you get the stuff. The second is that this stuff is one of the more hygroscopic things on the planet, and exotherms when mixed -- you have to add it really slowly to the water or it will boil explosively. It may be even worse than diluting pure sulfuric acid! Took me an hour to make a gallon, and starting with cold water, it was on the threshold of boiling the entire time as I added it a spoonful every couple minutes.
A nice trick, if you're going to drill your boards with a dremel drill-press (recommended) is to tell Trax to make guide holes in all the pads of about 15-20 mils. These act like centerpunches to guide the drill bit in, using the slop in the drill press to get that happening. Makes things go lots faster.
So, a step by step here:
Lay out the board. During layout, especially if you're working with some new parts (things like connectors are all wildly different and usually you have to get out calipers and try to make the right footprint), you print some 1::1 check plots to make sure your parts fit on the paper representation. That will save you some grief for sure. Also, you can check things like 90 degree connectors to make sure you got the pinout right with how they fold the wiring inside -- backwards connectors are all too easy to wind up with. Also, put some text on every board layer so you can later be sure you put the artwork on right side up during exposure -- I don't want to admit how many times I've made boards the wrong way when I didn't do this!
Make your artwork. I like laser printer art a little better than what I get from an inkjet, but it's truly a question of one marginal thing or another. I've known people to try and make two copies and tape them together in registration to get blacker blacks, for example, but I never do that, just do the exposure just so -- easier for me. I wrote a little perl/tk script that has a timer with the right number as the default, that shows a shrinking pie chart and beeps when timing out -- makes it easy.
Expose your board. If doing double-sided, you can do just one side, then drill a couple of holes to get good registration for the other side, or you can pre register your artwork by taping both pieces to a board scrap along one edge, then insert the board, and expose both sides before developing. That trick avoids slippage -- if you just tape them together with no spacer, they won't line up with a board thickness between them -- and you'll not be able to notice until too late. Here, I use an exposure frame I made from two pieces of glass, one glued to an iron angle, the other hinged to that, so when closed they are both flat, as the hinge is setup to have the 1/16" spacing between them. I clamp these together with cheap plastic spring clamps for exposure so nothing moves.
Develop your board - mix the developer according to directions for the first try -- you may want to adjust that once you get some experience. I put them in a flat tray, and rock the tray for agitation that makes it go faster and more uniformly, but also have been known to just rub on trouble spots with a fingertip or brush -- the manufacture isn't all that uniform, but what saves you here is that the photo sensitive layer is thick, and "linear". In other words, light exposure merely affects the rate of dissolution of the resist in the devloper -- even a non exposed board will eventually lose all the resist left in there long enough.
So, you can correct a little for exposure in the developer (none of this will be news to any film developer, it's about the same set of issues). I check development with Ferric Chloride etchant, it immediately shows any little bad spots. For the worst of these (as in, sometimes there's a thick spot or a bit of dirt in the resist) I'll just whip out an exacto knife under the microscope/magnifier and fix that.
Once you have that all working, you etch the board. Warm etchant works a lot faster than room temperature, and I've been known to preheat it in the microwave oven when I get impatient. Agitation is very important here. The low tech way is just to have a hook of baling wire, and lift and drop the board in the etchant tray, but the resist is very fragile, so you have to be careful not to scratch it. I've also built tall, wide, but thin tanks out of plexiglass and put an airstone (from the fish store) in there - but with ferric chloride, 'ware the fizz -- that stuff ruins almost everything it comes in contact with. In general, unless I've overexposed or overdeveloped the board a good bit, I'll leave it in the etchant for a few minutes after it looks done -- a thin film of Cu you can't see easily will really mess things up in some high impedance circuits later on. As I'm not doing plated through holes, I just make vias and then solder a bit of WW wire through them, or solder some components on both sides. Inelegant, but it works!
What I have found here is that this is by far the quickest way to get some medium complex thing going on and tested. A PCB is one heck of a lot easier to modify if you have some minor mistake than a perf board is, and you're not really going to put into service something on one of those plug in kludge boards. But if I need more than about 2-3 boards (unless they are tiny and surface mount with few holes) I go out to APCircuits for more -- they do such a nice job, cheap and fast, that I mainly do this for one-offs. Nowadays, some parts are only available in SMD with some oddball footprint, and you really can't practically prototype them with dead bug techniques at all. So for some things, you begin with a PCB, not end with it.
You can choose whether to leave the resist on there or not when done. It's easy to solder right through if left on there, but will come off easily too with rosin cleaner, acetone, or a lot of other things. Not really a solder mask material at all. If you're going to strip it -- do it before you drill the holes, as the little burrs will catch your solvent soaked paper towel and make a mess. If I'm not going to build the board right away, I leave it on to keep the copper underneath very clean and ready to solder.
I have tried the electroless tin plating solutions. The word is -- avoid. They don't work well and more often than not make soldering harder -- the opposite of the claim for them. If you need fancy boards, see the APCircuits link. I have found nothing that beats Glyptal from Caswell plating for coating boards that need low leakage and corona so far. If you get this and are using it in tiny amounts, put it in a canning jar, as the metal can seal will fail after a few uses. As this stuff isn't cheap, it matters a lot to keep your stock from getting hard on you.