My company uses VxWorks, MQX, Android, Windows CE and Linux. We're dropping VxWorks because it's costly and cumbersome. MQX is being replaced by whatever Freescale/NXP is pushing now, we put a lot of resources into the older version of MQX and aren't following them into their new incarnation. We use Android for special devices, but it seems to take a good amount of work to put it on custom hardware.
The OS that makes the most sense for embedded work nine times out of ten is Linux. It's widely used, documented enough, and has the most vendor support.
A good setup? You can get an AM335x EVM with an LCD, which is the same processor as a Rasberry Pi. I believe i.MX6 has an EVM with an LCD as well. Bottom line, you should talk to vendors, to see what they have to offer. Since it sounds like you have limited experience in this area, working with a vendor that will give you support is probably the most important thing.
Your developer tools are entirely dependent on your OS and chip. Ultimately, doing embedded work you're most likely going to use C/C++, but if you're on Linux or any modern operating system, then you have the ability to use a scripting language.