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

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)

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.

The .gitignore rule "Icon?" will also match directories such as
"icons/", at least on a case-insensitive file-system (this happened to
me on OS X 10.7). I only noticed this several days later because a
developer was complaining about missing icons in his repository. I don't
really know what type of files this rule is supposed to match, but I
guess the described behavior is not expected.

According to this (http://netbeans.org/kb/docs/java/import-eclipse.html#versioning) knowledge base article, the nbproject folder should be checked into the VCS in order to allow people to open the project without importing.

It is possible to run the project converter multiple times, which would generate new backup-directories (Backup1-Backupn) and logfiles (UpgradeLog2.XML-UpgradeLogn.XML)

gitignore files.

The behavior is documented in [1].
The prefix doesn't seem to be documented, but it is hardoced as described in [2].

[1]: http://www.gnu.org/software/emacs/manual/html_node/emacs/Interlocking.html#Interlocking
[2]: http://tekman.livejournal.com/79598.html