Although BWA is a very popular and well tested aligner, it’s hardly the only aligner around. There is an extensive list of open source and commercial short read aligners available on Wikipedia. Another collection can be found on the EBI webpage (there’s also information about the number of citations...
Although BLAST (Basic Local Alignment Search Tool) is not strictly a next generation sequencing tool, I use it regularly for a wide variety of tasks. Here are a few scenarios I use BLAST for: