One thing to keep in mind is that featureful GUI programs like Multi Gnome Terminal use many underlying system components. Things like excessive memory usage, or a keyboard that does not do what we expect, may have the root cause in the underlying libraries and utilities.
Below are some points that might be useful for troubleshooting or optimizing.
You can conserve resources by using the New Window feature from the GUI or command line, or the --use-factory command line option, when opening new windows, rather than starting a completely new Multi Gnome Terminal process.
Pixmap and transparent backgrounds will always use more memory than a solid background. A solid background should also be faster, since there is less going on.
Some versions of XFree, and some GTK themes, may not be good about freeing memory, leading to excessive memory usage. Notably, XFree 4.1 (and 4.0?), are known not to release all memory when transparent backgrounds are used. This is not a problem with 3.3.6, and apparently much improved with 4.2. Some themes may have similar problems, or at least aggravate the X memory leak situation. There is nothing that Multi Gnome Terminal can do to lessen this impact. If you experience unusually high memory consumption that keeps growing, please try a different GTK theme, and, if possible, upgrade to XFree-4.2.
Multi Gnome Terminal's rich set of features comes with a small price tag. Multi Gnome Terminal must spend more CPU cycles "watching" the terminal buffer (even non-visible ones) than other similar applications in order to provide some of these features. On modern, faster systems this should not be noticeable in all but the most unusual of circumstances. The impact of all this may depend on many factors, including your hardware, library versions, and how other system resources are being allocated.
Very fast scrolling or exceptionally busy screens may force Multi Gnome Terminal into overdrive. This may be more noticeable on low end hardware or during high system load periods. Consider using a non-pixmap, solid background color in such situations. This will help quite a bit. Re-nicing the process can make a difference too. In fact, you can set the shell that is running in the terminal to be re-niced automatically in Edit Commands, and start it automatically when it might be needed. Maybe call it "Nice Bash" ;-)