and the alt-tab icon too...

This is not possible AFAIK,

You may set LSUIElement of Terminal.app's Info.plist to 1. So you will hide your Terminal both from the Dock and cmd-tab list. TotalTerminal doesn't want to modifying Terminal.app's files, so you have to do it manually.

http://stackoverflow.com/questions/4154531/prevent-an-application-to-be-show-in-the-cmd-tab-application-cycle

One possible solution would be to let the user decide which app TotalTerminal should inject into, perhaps as an advanced setting or something. Then it would be possible to make a copy of Terminal, set it to agent and inject into that one, while regular terminal still had its Dock icon. Best of both worlds although it means an extra copy of Terminal lying around.

lesser known issue with this setup: it makes the preferences window very hard to interact with, as putting up the terminal will make the preferences window disappear

In 1.4.2 you can specify hidden tweak and TotalTerminal switches Terminal.app into UIElement mode during runtime.

defaults write com.apple.Terminal TotalTerminalHideDockIcon -bool YES

Not working for me in OSX 10.9, TotalTerminal 1.4.2.

Dock icon still visible, tried restarting the app, still there.

@popavo can you comment on this?

hmmm, with TotalTerminalHideDockIcon key set to true, it should just work. although sometimes setting defaults for an app that's currently running fails.
@aamaras try running do shell script "defaults write com.apple.Terminal TotalTerminalHideDockIcon -bool YES" in AppleScript Editor. But make sure Terminal is not running

Yep; ran it in AppleScript Editor and it works perfectly now. Thanks 😄

By the way, if people actually wants to CMD + Tab between totalterminal (v1.5.4) and other apps, you can still do defaults write com.apple.Terminal TotalTerminalHideDockIcon -bool NO and restart it.

Fantastic! It really works.