MEGA 4 or new version MEGA, is a good soft for the nucleotide alignment but you can also use perform it in NCBI website through BLAST.
It depends of the nature of the sequences that you want to align. I guess you want a complete suite with options of global, local and other kind of alignments. CLC Main WorkBench with the clustal plugin is a good option. But MEGA offers you a special kind of alignment that I like too much for coding sequences: the "Clustal (codons)".
It is really depends on what you are looking for. Clustalw and Clustal Omega is the most cited. MUSCLE is the most powerful. TCOFEE have different modules. MEGA, BBioedit and Jalview are stand alone program that will be faster with nice graphics for publication. You can also make combination. Anyway, you can download attached paper to learn more about multiple sequence alignment
Article Assessment of Molecular (Dis)similarity: The Role of Multipl...
speed：Muscle>MAFFT>ClustalW>T-Coffee；accuracy：MAFFT>Muscle>T-Coffee>ClustalW，The MAFFT is recommended to align sequence.http://blog.sciencenet.cn/blog-460481-706083.html
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