Sequence compression method / format
BAM is the current standard for sequence alignments, and can be used to store unaligned reads/sequences, but when used for unaligned sequences also contains unused alignment data that would bloat the file. 

An alternative way to compress a DNA sequence file is via 2-bit (or 4-bit encoding) which can compress the sequence content by 75% (in 2-bit encoding, each nucleotide can be represented by 2-bits in the file eg A: 00, G: 01, C: 10, T: 11). I do not know of a generalizable tool that will compress/decompress aside from rolling your own. Further, the data must be de-compressed prior to streaming it into any alignment/sequence software. For general purpose compression algorithms, bzip2 can outperform (at least in compression) other algorithms (eg zip, gzip)