Check out DipTrace. It's fugly though, running on OSX. But I think it's a worthy contender/upgrade/step-up from Eagle.
DipTrace is fugly on a Mac, it's true, but it does seem to work just fine. It's a native Windows app, so it looks fine there. There isn't a Linux version, but since the Mac version is just the Windows version packaged with Wine, I'd expect the Windows version could run under Wine on Linux.
The DipTrace free version is not limited on board size like Eagle's free version. Instead, it's limited on the number of pins--no more than 300 for the free version, and only two signal layers on the board (as many power and ground layers as you want). What I've seen (very little) and heard (a bit more) suggests that DipTrace is quite a bit more intuitive than Eagle, but no doubt YMMV.
KiCad is completely free, not just a limited freeware version. I've not heard good things about its usability, though I haven't run it myself.