This is simply a list of tasks and the tools I prefer to use in order to accomplish each task. I will also provide a brief explanation about why I choose that particular tool.
The List:
Local and gapped alignments: lastz
I prefer lastz because it is an extremely flexible tool with a multitude of parameters. There are too many to name but it is a really good multitool. When I am not performing a short read alignment, or a database search (blast on nt) then this is what I use. One specific feature I enjoy is that it can produce SAM files as output. It is not particularly fast, depending on the parameters of course, but in most cases this can be over come using simple parallelization.