aMSN (Alvaro's Messenger) may just be the most popular client for the MSN protocol, with an interface which resembles the MSN Messenger interface from Windows. aMSN offers a wealth of configuration options, allowing you to customise it to look just the way you want. By default it comes with six plugins, but many more can be downloaded and used. The same applies for skins, which you can fetch from the official website, then uncompress them into the ~/.amsn/skins directory. aMSN also provides webcam support.
Pidgin is the default IM client in GNOME (and Ubuntu implicitly). It is a universal client and supports protocols like Yahoo!, MSN (WLM), AIM, Jabber and it can be used even as a basic IRC client. I liked that it seems to support Yahoo! better than Kopete does. Pidgin comes by default with various plugins, to mention a few: history, mouse gestures, Nautilus integration, text replacement, and even a contact availability prediction plugin (hardly useful in my opinion but... at least it's available).
The default client for IM in KDE3 and KDE4, Kopete, just like Pidgin, offers support for all the major protocols out there, including Yahoo!, Jabber, IRC, WLM or Gadu Gadu. One of the minuses I found with Kopete is that it won't allow to send mass messages to a group which members are offline and it sometimes has problems setting your avatar so that others can see it. I don't know whether this is the protocol which changes or Kopete's fault. Although not Kopete-unique, one of the features I love is the ability to set a message queue and to be notified of new messages by flashing the system tray icon. It also allows tabbed-chat, so you can have a single opened window for all the active chats. Kopete comes with great support for a huge number of emoticon themes, which can be installed directly from within it using the kde-look.org website. It has support for plugins, including history, now listening plugin, spell checker or translator. The big minus regarding Kopete, at least for me, is that it seems not as intuitive at it should be, and sometimes the configuration options and the way you have to work with it is at least weird. Still, it is the client of choice for KDE.
Emesene is a client for WLM (Windows Live Messenger), featuring an extremely simple and easy to use interface. It comes with plugins like a spell checker, support for sound notifications, take screenshots and send them using the /screenshot command, conversation logger and a playing status which supports many audio players, including Amarok 1.4, Amarok 2, Rhythmbox, Banshee, Audacious or MPD. Emesene is a perfect GTK alternative to aMSN and Pidgin for MSN users.