The reason why there are a lot of formats out there, is that every format had appeared by specialists in a specific field, for example specialists in phylogeny use Phylip format...etc
So before you use any format you have to ask yourself questions like: is this format supported by the program i'm running, is it easy for me to modify in it, is it widely accepted...etc.
Some of the most popular multiple sequence alignment formats:
1- FASTA: a text format that's widely accepted and its easy to read and modify.
2- MSF: (Multiple Sequence Format), the most popular, supported by most programs, easy to read and difficult to modify.
3- ALN: produced by ClustalW, easy to read and widely supported.
4- Phylip: text format, supported by most phylogenetic packages.
Any question, u're welcome.