I frequently want to make tweaks to one window, and I just can't stand having to make a new set of Preferences every time a window disagrees with the established settings. Since the sets contain everything (colors, terminal attributes, long lists of key mappings, etc.) there are potentially a lot of things to redo.
Also, what's bizarre is that opening a saved file has the side effect of automatically creating a new, permanent set of Preferences. There isn't much point in having files if Terminal insists on re-storing everything as Preferences anyway.
When Leopard came out, it had a Terminal.app that fixed essentially all my issues with the previous Terminal.app, including having tabs, etc, and it hardly uses any resources at all, and stays open without crashing for weeks at a time (in fact, I don't think I've ever managed to crash it). Now that there's a copy-on-select plugin for SIMBL for Terminal.app, it's just about perfect.
Try GNU screen or tmux.
Note: I am using zsh with my term declared as xterm.