I personally use gnome-terminal as my terminal emulator. Using gnome-terminal, I run GNU Screen (byobu to be specific) in order to work with multiple windows. You can become really efficient with it. I use GNU Screen because I often have long-lived terminal sessions that I can check on or come back to later.

gnome-terminal running byobu (showing only one window open)

You seem more interested in a graphical solution for managing terminal windows. For this, I highly suggest the terminal emulator Terminator, which supports multiple windows without the need for a multiplexer like GNU Screen. You can split it horizontally and vertically as much as you like and there are even tabs. If you just feel like running lots of terminals, Terminator is really good.

Terminator (showing multiple Terminator windows open)

What I believe you are looking for is a fixed asset management system, you can find plenty of Linux based fams, but a lot of them are designed for enterprise so you will find that they are interesting to set up and most likely web based.

I recommend checking out some of the items in this list:

http://sourceforge.net/projects/fams/