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Some people don't like the X-style copy/paste semantics in which selecting text automatically copies it to the clipboard and clicking a mouse button is enough to perform a paste. These semantics make copy and paste something of a hair-trigger operation - a misplaced click and drag can destroy valuable data from another application which you'd had in the clipboard, and equally a misplaced mouse action can paste all sorts of weird text into an unsuspecting PuTTY.
An alternative would be to adopt conventional Windows-style copy and paste keys: selecting text has no direct effect, Ctrl-Ins copies it to the clipboard, and Shift-Ins pastes it. (We actually already support Shift-Ins to paste.) We could also support ^C and ^V to do the same things, although this would be unlikely to be very useful since those key combinations are almost always needed to perform server-side actions.
Another possibility is that perhaps the mouse-clicks-only copy and paste could still work within a single PuTTY window, but Shift-Ins and Ctrl-Ins would be required in order to interact with the main Windows clipboard. This might strike a balance between convenience and safety (although it requires the user to keep in mind that there are two separate clipboards, so it wouldn't make a good default configuration).
Other options would be to introduce Copy and Paste entries in the System menu (like DOS boxes), or in the toolbar (if we ever add one). And if the current mouse-driven pasting is disabled, then that would leave the right mouse button free to bring up a context menu which could contain Copy and Paste as menu items.
These would certainly be configurable options if we do them at all - enough people, including the developers, like the copy and paste the way it is that we would never consider removing the current behaviour.
Update: as of 2003-11-21, there is a new mouse-handling option whereby the right button brings up a context menu containing a Paste option, rather than pasting directly.
2017-12-17: most of the above is now possible (except that the keys involved are Ctrl-Shift-C/V).