It's a trivial thing to automatically start application during the boot. But in fact not that much. It's your init's job to do this. It should be something easy (huh systemd ?). Starting a command inside tmux isn't native to current inits. Here's how to do it.
First we will start with OpenRC init file (sorry i won't tro^wtalk about systemd). So in /etc/init.d/tmux you put the right shebang and in the start() section you put :
start-stop-daemon -u lord -S -b -x /home/lord/tmuxboot.sh -d /home/lord > /var/log/tmuxboot.log 2>&1
Here we've just told openrc to launch the /home/lord/tmuxboot.sh script from /home/lord/ with the lord user.
Now we have to populate tmuxboot.sh to instruct tmux what to do. It's a simple shell script. The trick is that tmux can take commands from outside the session.
#! /bin/sh tmux new-session -d -n rtorrent '/usr/bin/rtorrent' tmux new-window -n Htop '/usr/bin/htop'
It's self explanatory. You can put many things in this script. It's really nice to be able to get the full output and backlog from commands launched inside this.