In GNOME Shell 3.2 you can reply to chat from the popup notifications, but that only works for Empathy by default. So here is a GNOME Shell extension that does the same thing but for Pidgin.
Pidgin GNOME Shell extension is easy to install but to make it even easier (and also get updates without having to run a bunch of commands), I've uploaded it to the WebUpd8 GNOME3 PPA.
Add the PPA and install Pidgin GNOME Shell extension in Ubuntu 11.10 Oneiric Ocelot using the following commands:
sudo add-apt-repository ppa:webupd8team/gnome3 sudo apt-get update sudo apt-get install gnome-shell-extensions-pidgin
Also install GNOME Tweak Tool if you haven't already:
sudo apt-get install gnome-tweak-tool
If you don't use Ubuntu or don't want to use our GNOME3 PPA, install it manually using the following commands (firstly make sure GIT is installed):
cd git clone https://github.com/kagesenshi/gnome-shell-extensions-pidgin.git mkdir -p ~/.firstname.lastname@example.org cp gnome-shell-extensions-pidgin/* ~/.email@example.com/
Once installed, restart GNOME Shell (press ALT + F2 and enter "r" or log out and log back in), then activate the extension using GNOME Tweak Tool (shows up as "Advanced settings" in the Activities "menu").
Tip: to avoid getting both the standard Pidgin notifications and the new ones, in Pidgin select Tools > Plugins and uncheck the box next to "Libnotify Popups".