Let me introduce my desktop...
Visual Studio Community 2013
This is my base development environment. I write code on this environment, build Windows version of uoYabause, and test it on Windows. After test is passed, build Android version( using ninja and Android Studio), then test it on SHIELD TV. NVIDIA Nsight is also installed. This frame debugger makes graphics programing much easier. I can't live without Nsight.
Light Capture
This is the video capture software connected to my real SEGA Saturn. With this I can compare emulation result and real device result.
Notepad++
This is a good editor which has many plugins. I write code located out of Visual Studio using this.
ComEmu
This is a terminal emulator which has much functionality. I use this at many scenes, building source code, connecting to web server, connecting to android devices, and seeing logcat.
NASM2 running on VMware
This software is connected to my real SEGA Saturn development environment (Cart dev), and can load binary, run it and debug it. This software is very important to analyze difference between real SEGA Satan and emulation.