Not a question with an easy answer. I am using the Full Keyboard app, but I really don't like it. The best would be if the terminal itself would implement an easy way to input keys like ctrl alt and escape.
There is a bug filed with connectbot, which is the terminal emulator I use, and I have added my voice to the clamor for a solution, but who knows when that will happen. If you are an android developer you might give the source of your terminal a hack and whip up a patch...
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