Do you mean log channel/query/dcc chat windows? You can with any of these:

-file/options/irc/logging

-click in upper left of the window you want to log ( or click alt key and - key) and choose logging

-in the window you want to log type /log on

- /log <on|off> <window> [-f filename]
Turns logging on and off for a window, if you specify a filename the logs file dialog is not popped up.