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Use of the System tray. So many people have requested this that I think it's a genuine desirable feature, but I don't want it to bloat the core of PuTTY. Therefore, it should be implemented using a separate program. There are a variety of programs out there already that do this. Here are some links to them.
There are also third-party versions of PuTTY which do this directly; see our Links page.
Audit trail for this wish.