Like I said, there's a second X11 clipboard that does work like Windows' clipboard. It's often not very useful. though, since many apps don't support it, xterm being high on that list. There's actually a Sun Java doc about X selections, but it unfortunately doesn't list best practices. Perhaps before highlighting the text you could copy the Primary Selection to the Clipboard Selection. Of course, then you might overwrite something important in there. It seems like the way they talk about it that you ought to be able to highlight without registering the selection with X. Maybe there's some low-level flag you could pass to it to keep it from asserting itself.

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What happens if you want to copy a block and paste on top of another block?

You can't do that with the Primary Selection method. When you paste in that paradigm, you never replace, only insert, sometimes at the mouse pointer, sometimes at the text cursor, depending on context. In practice, this is usually 100 times faster than the Windows method for simple copy-and-paste.