Hi guys, just in case this will be helpful for someone, I successfully built aquaria with both gcc and ekopath.
gcc (Gentoo 4.6.2 p1.0, pie-0.4.5) 4.6.2
PathScale EKOPath(tm) Compiler Suite: Version 4.0.12
With gcc it just worked, just cd into an empty directory and run
cmake <path to aquaria> -DCMAKE_BUILD_TYPE=Release
make -j<your number of cores>
(if you don't know how many cores you have just run make alone, or "make -j$(cat /proc/cpuinfo | grep -m 1 'cpu cores' | grep -Po \\d)" note that the higher the number you put, the more memory you will need)
Once finished you can copy the binary to wherever your data files are and delete this temporary dir. The code will still be kept.
With ekopath some fixes were needed, but I still think the coders did a great job in writing high quality code. Bravi! Enough said, down to the fixes:
in the CMakeLists.txt I added those two lines:
SET(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} -O3 -OPT:Olimit=0")
SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -OPT:Olimit=0")
Those are optional. You can drop -O3, you would still get a good result. The second option, -OPT:Olimit=0, shuts down a warning about the optimizer running out of memory and giving up in some cases, but the build would still be successful. Make sure you have enough ram if you use this option (I needed around 1 GiB and I ran make -j2). To save up memory you can run make without the -j option.
Second fix is in aquaria/BBGE/Joystick.cpp, as the compiler would complain about close() and write() not being defined. The prototype for those functions are in unistd.h, so open Joystick.cpp, go down where you see #include "Core.h" and add the following right after that:
#ifdef __LINUX__
#include <unistd.h>
#endif
That's it, run cmake with the following command:
CC=pathcc CXX=pathCC cmake ../aquaria/ -DCMAKE_BUILD_TYPE=Release
run make or make -j and wait for your steaming hot binary

In my case, gcc made a 3 MiB binary, ekopath a 8.7 MiB one. Building with intel compiler should be easy enough, you can try if you want, just replace pathcc with icc and pathCC with icpc in the previous command. Me, I'm happy enough with my ekopath binary. Have fun!
Edit: I see some people are having issues getting the code. Just install mercurial from your package manager or get it from
here, cd into a new dir where you want the code to be downloaded and run
hg clone
http://hg.icculus.org/icculus/aquaria/A new directory called aquaria will be created and you will find the code inside. You can then remove mercurial if you want.