Next, FreePCB or equivalent Linux program to layout PCB's, any suggestions.
EagleCAD does have a version for Linux that works well. Not exactly "free", though (they have a "free" version, but it is limited, and the price escalates quickly - but I have heard that if you are serious about using it - ie, for business/money-making purposes - it will pay you back quickly):http://www.cadsoftusa.com/
For true open-source and free, there is:
GPL EDA (gEDA) - http://www.gpleda.org/
KiCad - http://www.kicad-pcb.org/
Both have their pluses and minuses. gEDA has a very, very steep learning curve, but if you can figure it out, you're pretty much set to do anything. KiCad has a less steep learning curve, but isn't as powerful as gEDA. Both are fairly mature, though.
Oh - one other "up-and-coming" which is more for "n00bs" but is interesting nonetheless:http://fritzing.org/
It is basically to EDA what the Arduino is to microcontrollers; it aims to make EDA very, very easy. To that end, it not only does schematic capture and PCB layout (and you can export to have Fritzing route/etch the PCBs for you), but it also does "breadboard" capture (and keeps the netlists in sync, to a certain extent). It tends to get people uptight, though, because people will post the breadboard "schematics" which are very difficult to follow, and also tends to make some think that there isn't any learning of how to read/draw true schematics. But I would check it out a bit at least.
I could give you a ton of other links to various other resources (not all free, not all linux, but all relating to EDA), but those are the "major three" to get you started.