Desktop
General Tools
Internet
Terminal: putty
File Transfer: WinSCP
Browser: Chrome
Productivity
MS Office: Word, Powerpoint, Excel
Notetaking: OneNote, Google Keep
E-mail: Google Inbox (web)
Calendar: Google Calendar (web)
Reference Management: Endnote, Mendeley
PDF: Adobe Reader
Development
Editor: emacs
ess (R formatting mode)
Add the MELPA package repo to emacs (https://melpa.org/#/getting-started)
Install ESS package
Unix tools: cygwin (see below)
Stats: R
Other languages/interpreters: Java
Cloud Documents
OneDrive, Google Drive
Communication
Skype
RSS: Feedly
Misc
Spotify
Cygwin
Cygwin has been an old friend, bringing a unix environment to the Windows boxes I've used for quite some time. They implemented a lot of the unix OS layer in a DLL, making it so that most unix apps can compile directly via the configure/make (via native gcc/g++ ports). There is also a repository of pre-compiled binaries that can be installed, which are the packages listed here. There is some thought in my mind of trying out the Linux subsystem on windows.
can install without admin rights: use the flag "--no-admin" when running setup-x86_64.exe
Development environment
gcc/g++/make
awk
python
perl
Internet Utilities/Terminal
openssh
X11: xorg-server, xinit, xorg-docs, xlaunch
For putty to be able to forward X11: startxwin -- -listen tcp
rsync, wget
Compiled
These will probably need to be compiled separately
data manipulation: datamash
cygwin - use the datamash.exe from: http://download.savannah.gnu.org/releases/datamash/windows-binaries/cygwin/
genomics: bedtools
cygwin compile: add "-D_GNU_SOURCE" to CPPFLAGS and change CXXFLAGS "-std=c++11" to "-std=gnu++11". Depends on zlib, bz2, lzma