There's Applescript support, so you could probably cobble together a script that'd launch your multiple windows & commands.

There's also Window->Save Window Arrangement, but I believe that only allows for a single arrangement.

Feel free to add a feature request at http://code.google.com/p/iterm2/issues/list (There's plans for eventually moving everything over to github, but the issues will get migrated too)

I'm working on improving the preferences UI and back-end, but I'm learning obj-c and Cocoa as I go, so it's a slowish process :)

I've created a quick fork of tmuxinator (originally used for defining sessions for tmux) to also generate iTerm setup scripts: https://github.com/dkastner/tmuxinator

I use screen for that, although scripting it is a pain in the ass. I'm considering trying tmux out.

iTerm2 currently supports a single group at the moment (called a Window Arrangement). If you need more than one, then applescript is your best bet for now.