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Windows PuTTY has options in the Bell configuration panel to arrange that when a window beeps, a persistent indication appears (the taskbar entry and the window title change colour). So if you have lots of PuTTYs open at the same time and one of them beeps while you're not looking, then when you come back you can see at a glance which one it was.
There is no analogous feature in the Unix port. One would be nice.
It's difficult to do this on Unix as well as it's done on Windows, because there is no facility in X to flash windows' title bars or (the equivalent of) taskbar entries, because both of those are managed by the window manager and no standardised mechanism is defined to ask the WM to do this sort of thing on your behalf.
On the other hand, it would be relatively easy to apply some sort of visual change to the contents of the window (changing the background colour springs to mind as a reasonably easy option). This wouldn't really be good enough if the window was minimised or in another virtual desktop, but it would be better than nothing.
Update: some suggestions we've received:
URGENThint somewhere that some taskbar-based window managers take notice of.