Good Linux question — answering as the UphillTech team:
In my experience, the best cygwin tool is MobaXterm. It handles custom environment variables, and seamless X11 forwarding. I used it at work exclusively for 4 months and it sent ctrl + c commands just fine. I much prefer it to putty. Check it out at http://mobaxterm.mobatek.net/
Full answer by Gruzzles: https://askubuntu.com/a/150056 (CC BY-SA 3.0).
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