MUSCLE Multiple Sequence Alignment. Also has a nice web interface to submit jobs directly online

MAFFT Multiple Sequence Alignment program for unix-like operating systems. Alternative to MUSCLE

t-coffee Multiple Sequence Alignment. Alternative to MUSCLE

clustalW2 Multiple Sequence Alignment. Alternative to MUSCLE

MEGA. integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence time. Fantastic GUI.

proprietary software.