Currently 64-bit Linux distributions are stable and well established so there are virtually no problems in opting for a 64-bit system.
However, some MATLAB Linux versions, notably the student version, only exists in 32-bit and it is not so obvious to get it installed in 64-bit Linux environment.
Here’s how I got it done (MATLAB R2009a in Ubuntu 10.04 Lucid):
1) Install some 32-bit libraries:
sudo apt-get install ia32-libs lib32ncurses5
2) Mount the CD (e.g. open the content in a file manager)
3) Install MATLAB, force to use the 32-bit executable:
sudo /media/cdrom0/install_unix.sh -glnx86
Install matlab to some convenient place, typically
/usr/local/matlab (assumed here).
The installation will fail, complaining about 64-bit java.
4) Fix the java problem (change the path according to your installation):
sudo ln -s /usr/local/matlab/sys/java/jre/glnx86/ /usr/local/matlab/sys/java/jre/glnxa64
5) Register your matlab
6) You can now run MATLAB: