I work in a research lab where we occasionally need to develop electronic driver boards for quantum cascade lasers. The type of signal these handle are digital data streams up to around 10 MHz and output drive current up to 100 ma or so. The board needs to interface with Altera development boards using their proprietary hsmc connector. We have some preliminary designs that work on a soldered breadboard, but the lack of a proper PCB is causing ringing and overshoot, etc. (there are some SMDs involved). Since I'm primarily a software engineer, I'm looking for a basic how-to on spining prototype PCBs using modern tools. Any help appreciated.
Try DesignSpark (it's free) from RS. It's based on Number One Systems' Easy-PC, which I used for many years. It generates standard Gerber and Excellon drill files which can be sent to any PCB supplier. You need to set it up for your supplier's design rules (track widths, hole sizes, etc.) of course, as with any PCB software.
I actually use Pulsonix, from the same company responsible for Easy-PC and DesignSpark. It's excellent, but it starts at $2,000.
For your PCBs, I recommend PCB Pool. They aren't the cheapest, but their boards are very high quality, and their customer service is superb if there are any problems.
For the software side take a look at KiCAD, it's Free and runs on Linux, OSX and even Windows, it's about as clunky as any other EDA package, but you can't beat the cost and it has no artificial limitations.
For the fabrication side take a look at ITead, they do really cheap double sideded PCBs in about two to three weeks including shipping: https://github.com/dren-dk/HAL900/wiki/Quirks-of-PCB-manufacturing-at-ITead
A few months late, but if it helps, I was in a situation that sounds similar to yours and we chose Eagle and had satisfactory results. This was also a startup-type situation, me and a friend. We had intended to just build hand-soldered breadboard prototypes but it became so tedious that we just decided to get ambitious and learn PCB design. We are both software guys by trade, my partner had some hobbyist electronics experience but board design was not something either of us had experience with. We went with Eagle because it's (relatively) cheap, supports Mac (the software side of our project is Mac-based), and has some traction in the hobbyist community (i.e. parts libraries available for a lot of hobbyist stuff, like SparkFun's Eagle libraries).
I went through the RPC Electronics Eagle tutorials and did my first board layout in a day or two. It was a super-simple design to get our feet wet, no components, just a breakout board to convert a connector to pins, but we wanted to have something manufactured to see what would happen. I also used SparkFun's tutorials on Eagle and their guides to PCB layout and preparing designs for submission.
From there we moved on to a small embedded system based on an ARM Cortex M3 microcontroller. Had some peripherals, several connectors, buttons, switches, power, clock crystal, JTAG port etc. Not a super complex design, but it is a small computer system and it works. Cribbed a lot of it from the schematics for our MCU development kit but hey, that's why the manufacturers provide all that info. Everything fit on a 4"x4" two-layer board, although two layers was probably pushing our luck with that MCU.
I just checked my project log and it was 14 work days from watching the Eagle tutorials to submitting the motherboard to the board house. We use PCB-POOL, they seem to have the best price/turnaround time ratio for what we need and they accept Eagle files directly so we didn't have to go through the Gerber generation process. They'll also throw in a solder stencil for SMD parts for free if you need it, and if you need it that's a nice bonus. Not every day was spent working on the PCB designs full-time either, so in retrospect I consider that a pretty good turnaround time to go from having no idea what I was doing to sending my first embedded system motherboard out for manufacture.
Eagle definitely feels a bit clunky and low-rent, and I would certainly love to have licenses for the "real" EDA tools magically appear on my computer free of charge. But if you are ambitious and willing to learn and want to get some stuff made you can just learn how to use Eagle and make it happen.
We bought the standard package with layout + schematic + autorouter. If you are pinching pennies I would say drop the autorouter and save the $249. There is a free autorouting tool, FreeRoute, that you can use with Eagle pretty easily and it's better than Eagle's autorouter. I ended up using FreeRoute to route the first rev of the board because it did a better job and routed stuff that Eagle failed at. In the end though, you'll want to learn how to route manually. It's intimidating and you have to start small and commit to flailing around for a couple days having no idea what you're doing and thinking you're going to trash your layout at every turn, but you get used to it and it's worth it.
Last bit of advice, whatever tool you pick, just pick it and design a board and have it made. If you just commit to doing it and make something, I think you will be surprised by how easy it is.
I have share online EDA tools: PCBWEB and EasyEDA at [question]: Schematic capture/PCB layout program recommendations.