Because files and directories starting with a `.` are not ignored in general.

Vim creates buffer swapfiles starting at .swp for buffers that are
active but untitled and unsaved.

Changed line matching vim swapfiles to use all names it will create as described in http://vimdoc.sourceforge.net/htmldoc/recover.html#E326

See http://en.wikipedia.org/wiki/Windows_thumbnail_cache#Thumbs.db

It contains project specific configuration, and should therefore by
checked into version control (as documented on
http://www.sublimetext.com/docs/2/projects.html)

Include .netrwhist, the user's history and potential privacy concern. See: http://stackoverflow.com/questions/9850360/

Including mexglx, mexa64, mexmaci64, mexw32 & mex64 (see
http://sfwn.in/FxbE for official list from Mathworks).

Org-mode stores archived TODOs from todo.org into todo.org_archive. It also
creates .org-id-locations in some cases.

*** .externalToolBuilders/
This directory stores project-specific launch configurations for external tool builders, such as ant tasks that have to be executed to fulfill the build lifecycle

*** *.launch
It is possible to store "eclipse launch configurations" in external files. These (XML-)files may be stored anywhere within your projects and will be discovered by Eclipse automagically.