Well, at the risk of sounding redundant, I'd start with FSAutostart to shut down the stuff running in the background...
How many Icons do you have running in your system tray, by the way?
I also modified the FS9.cfg file so that the fast-food restaurants aren't there. This really helped my framerates.
Quoting from the main fourm...
Heya HSV,
A common issue with FS 2004 are all of the restaurant signs clogging the memory (especially in urban areas). This over a period of time can cause frame rates to drop.
Two things that you may do to avoid this:
1. In the main FS2004 folder you will find a subfolder called Autogen. In that folder there is a single file named Default.xml . I renamed this file to default.BAK.
2. Find the line in the [Graphics] section of FS9.cfg file that reads TERRAIN_USE_VECTOR_OBJECTS=1 and change the 1 to a 0 so that the new line reads TERRAIN_USE_VECTOR_OBJECTS=0 .
You'll be missing some fastfood restaurant signs, however, you should see both an end to the poor FPS when returning to the airport to land and an increase in framerates when flying in the city.
Personally, I didn't notice the Fast Food reastaurants being gone very much, but I
did notice the difference in framerates!
I also have gotten rid of the default AI and replaced it with Project AI. I have the traffic set at 72%...which gets me great framerates even with the LET when landing at O'Hare...