Settings

Add CR/LF to copied text - When copying data from a session window, automatically add in carriage return/line feed data at the end of each line. This means that lines that were wrapped in the original copy will be wrapped in the paste as well. This behavior can be changed at the moment of copying by holding down the shift key. This will reverse the setting specified here.

Confirm quit when connections open - If you attempt to close PenguiNet while you still have connections open, this option will cause a confirmation dialog to appear before the close will happen. This is useful if you accidentally hit the close button.

Jump to bottom on key press - If you have scrolled back a session window, typing a character in that session window will cause the scroll to jump back to the current line.

Check for PenguiNet updates - With this option enabled, each time you start PenguiNet, an auto-update check is fired off. This check makes an http (web) request to http://www.siliconcircus.com/penguinet/autoupdate.php. This page indicates to PenguiNet whether or not a new version is available, and if so, you are presented with the option to download the update.
There is no security risk posed by leaving this enabled (no information is sent with the auto-update request), but if you prefer to disable the auto-update, un-check this option.

... lines of scrollback - This setting effects all session windows. A large scrollback will consume considerable amounts of memory, so a reasonable value for this would be 200 lines.

Emulate SDI - When this option is enabled, PenguiNet will act like an SDI application. This means that new session windows will open outside of the main PenguiNet window and can be individually controlled. The Window menu option will no longer be available, since those options do not apply.
When enabling or disabling SDI emulation, the change will not take full effect until PenguiNet is restarted.

Minimise to systray - This option will cause PenguiNet to minimise to the system tray instead of to the Windows taskbar.

Show 'Connection closed' messages - If you un-check this option, when a connection is closed normally, the session window will automatically close and no message will appear. If the connection is closed abnormally (due to a timeout, for example), you will still receive a connection closed message.

Open profiles window when started - This will cause the profiles window to automatically open when launching PenguiNet.

Show splash screen - This option is only available to registered users. When un-checked, the splash screen which appears upon starting PenguiNet will no longer appear.

Use middle mouse button as paste - Un-checking this option will disable the functionality which enables a paste to be done by pushing your middle mouse button, if available. On a wheel mouse, this is typically achieved by pushing the wheel down, rather than rolling the wheel.

Proxy

PenguiNet supports SOCKS 4 and SOCKS 5 proxy servers. Configuration details entered here will effect all profiles unless explicitly disabled on the Connection profiles - options tab. If you need to use a SOCKS server, contact your system administrator for the information if necessary.