I regularly make double-sided home-brew pcb boards for prototypes. Here are a few tips I have learned the hard way:
1. Don't bother with the special "transfer paper" for iron-on. Any paper you can run through your laser printer or copier will work. Just iron the paper onto the cleaned (steel wool) copper clad board till the toner sticks, and then soak the board in water till the paper gets soggy. Peel and rub the soggy paper off the board, leaving the toner. Don't iron with too much pressure or heat because the toner will squish/run. So far I have found that paper like "Time" magazine pages works best. The only problem is that magazine paper has guff printed on it that makes it hard to see your pcb image. My paper store sold me some 60# glossy white paper stock that works great. (note that this is thinner than standard 20# bond)
2. You can use the free Protel EasyTrack and EasyPlot software for layout and printing. (you can also download it at AP Circuits). It is a DOS program, but the price is right. Use 12 mil tracks and 62 mil pads so that you can run tracks between DIP pads. Print out pcb images with 20-25 mil pad holes so that when you iron the circuit onto the copper, the holes do not fill in. You will need some hole opening to center the drill bit. Remember to "flip" your top/component layer image when you print it, and to put any wording ("strings") on it to identify the board and its components in copper.
3. Get the etch solution up to 100 F by soaking it and the etching pan under the hot water tap for best results. You can etch a board in about 5 minutes with the hot solution, but it is not hot enough to give off too many noxious fumes. Once you have etched the board clean off the toner with solvent and steel wool and then immediately coat the board with a little "Bruce 1-Step Acrylic" liquid floor wax to stop copper oxidation. This is VERY IMPORTANT if you do not solder the board immediately. The wax burns off with no residue at solder temperature.
3. For hole drilling, use a Dremel tool and the $50 accessory drill press. The high rotational Dremel speed is important because the small bits cut best when their edge speed is kept reasonable. To keep from going blind, get one of the big illuminated magnifiers that clamp onto the side of your work table. Carbide drill bits cut best although they are very brittle and break easily. Buy the carbide "resharps" or used bits for under $1. On your pcb layout program, set the hole size as large as you can (but not bigger than your pads!) because the ironing process will tend to fill in the hole, and you need some hole left in the copper to center the drill bit. If you try to drill a hole in a pad where the hole is filled in, your carbide bit will slip around the pad and probably shatter.
4. To line up the two side of a double sided board, iron on one side, drill out some pilot holes, then line up the second side by holding it up to the light, and iron it on. Then soak the paper off both sides. Note that since you will not have plated thru holes, you will have to remember to solder some wire through the vias, and that traces on the top/component side of the board will have to be soldered on top to component/socket legs.
5. When you have debugged you board, you can get a professionally produced two-sided board with plated through holes for less than $100 from AP Circuits. One source for carbide drill bits is Hosefelt Electronics 800/524-6464: $3.25 gets you 5 resharps, and I use the #65 (.034") or the #61 (.039"). Double sided pcb stock (1 oz copper on 1/16" FR4) and etchant is available at Radio Shack, but you can get the board price down to about 10 cents/sq inch if you get large sheets from places like Hosefelt. I cut it up with a band saw. Throw away your Radio Shack $5 soldering iron and get a variable power (or better yet variable temp) iron with a small tip. Hosefelt sells the WLC100 "Weller" station for $39.95 and 1/32" conical tips for $3.99.