One odd thing about MSFS is that runway lights tend to be rendered too large. Use these fs9.cfg file settings to give them a more realistic appearance.
 

[DISPLAY]
RUNWAY_LIGHTS_SURFACE_SCALAR=1.0      //scales edge, center, end, touchdown, runways
RUNWAY_LIGHTS_VASI_SCALAR=1.0              // scales VASI lights
RUNWAY_LIGHTS_APPROACH_SCALAR=1.0   // scales approach light bars
RUNWAY_LIGHTS_STROBE_SCALAR=1.0        //scales RAILs and ODALs

Making the value smaller will reduce the apparent size of the light. Try setting all of them to 0.5 as a starting point. This is a good one.

Not owning a P4 or a dual system I haven't been able to test this out but it should work.

After starting FS, go into task manager (CTRL_ALT_DEL)
Select Processes tab
Right click on FS9.exe, select "Set Affinity"
Disable one of the two check boxes so that FS9 only runs on one virtual CPU.
Do the same on any other running utilities and select the other virtual processor.

Users who run a lot of extra software report as much as a doubling in frame rates. This, of course, assumes that hyperthreading is supported and enabled on your motherboard and BIOS settings.

An even better (permanent) way of constraining FS9 to run on a single virtual CPU  is by using the Microsoft IMAGECFG utility (an older NT/2000 utility that works fine in XP -- do a google search). Command syntax (in a Command window):

IMAGECFG -a 0x1 <your FS directory>\fs9.exe

This writes a processor affinity mask into the executable. 0x1 specifies virtual CPU 0, 0x2 specifies vCPU 1, and 0x3 uses both 0 & 1 (default). FS will always run on the specified virtual CPU(s) from that point on.
Do the same with the other utilities but assign them to the other virtual CPU and you're all set.

Find the [STARTUP] section of the fs9.cfg file and change the value of the following line to 0

SHOW_OPENING_SCREEN=1
 

To change to this display when you hit CTRL+Z add the following line to the fs9.cgf file under [MAIN]

AVE_FRAME_RATE_DISPLAY=1

Add the following line to the [SIM] section of the fs9.cfg file.

SHOW_BRAKE_MESSAGE=0

The default setting for the maximum mesh resolution is 75 meters. To properly display custom mesh change the following line in fs9.cfg

TERRAIN_MAX_VERTEX_LEVEL=19

The proper values are - 18 = 150m, 19 = 75m, 20 = 37m, 21 = 19m.

By disabled the AGP Texture Acceleration within MSFS you will see an increase in frame rate on some systems. To do so add these two lines under the last display device heading listed.

TextureAGP=0
PanelAsTexture=0

If FSAA may cause problems with this setting. If that's the case then invoke FSAA from your video driver setup rather then from within MSFS.

Add the following lines to the Autopilot section of each aircraft's CFG file that you want to behave this way.

use_no_default_bank=1
use_no_default_pitch=1

This is caused by some kind of bug in FS2004. Apparently, Auto-gen keeps accumulating objects even when the objects are no longer visible. MS will need to issue a patch for this but in the meantime there is a workaround that does not impact visual quality of the scenery very much.

To explain, FS2004 has 2 additional types of Auto-gen beyond what was available in MSFS 2002. You have the regular Auto-gen that is mostly assigned by the .agn files like FS2002. In addition you have Auto-gen that is assigned in the terrain.cfg file, bridges, high-tension towers, highway signs, etc. These objects can be disabled individually in the terrain.cfg. They can also be completely disabled by changing this line in your fs9.cfg under the [GRAPHICS SECTION].

TERRAIN_USE_VECTOR_OBJECTS=0           //0=off, 1=on

Another type of Auto-gen is assigned by the default.xml file in the Auto-gen folder. This is where the fast food buildings and other types of new Auto-gen objects are added. The default.xml file can be edited to get rid of certain types of objects, you can also disable this type of Auto-gen on a texture by texture basis with the annotator tool included in the FS2K2 Auto-gen SDK. You can also disable all of these types of additional objects by renaming the default.xml to:

default.xml.bak

Disabling both (by renaming the default.xml file AND setting the option in the cfg file to 0) will prevent auto-gen from accumulating and improve performance significantly. Enabling only one of the options will not slow the sim very much and auto-gen data will not accumulate. However, having both these enabled will cause massive slowdowns, especially when nearing airports or when slewing.

The best recommendation is to leave TERRAIN_USE_VECTOR_OBJECTS set to 1, but rename the default.xml file to default.xml.bak. The bridges, high-tension towers and highway signs add a lot more to the scenery, visually, than the fast food buildings do.

This is a big fix that everyone should apply until MS takes care of the problem.

Run MSFS in a window that you’ve manually expanded to fit as much of your screen as possible while maintaining round instrument faces. With some video cards you’ll gain a few FPS this way. Not all systems will respond to this but it can be a life saver on a marginal machine.

If your 2D panel is a rate hog (many are) try dragging it down until just the main instruments are showing. On the stock 172 this will give you a boost in FPS while leaving the instruments visible. You’ll also need to drag down the lower edge of the outside view when you do this. It’s not as much of a boost as when going to the mini-panel or the clean outside views but it helps. People with good Go Flight panel setups might even consider building custom cut down panels that don’t duplicate functions that are being handled by the Go Flight hardware. It would be worth the trouble given the potential performance gains that are possible.

Use Viagra.....just kidding.

Always reboot before starting an MSFS session. Because Windows is Windows, running and shutting down even a few applications before starting MSFS can have a noticeable impact on your frame rates, especially if you have less then 512 MB of system RAM. Always boot fresh and turn off un-needed background programs and processes. This can make a huge difference so it's worth doing.

If at all possible try to reserve a partition on your hard drive that's used for MSFS and it's add-ons only. One of the major causes of stuttering is accessing the hard drive for new textures, mesh data or objects. By giving MSFS it's own partition it will be easy to keep it defragmented and it will minimize the affect that drive accesses will have on your performance.

Checking this box in the hardware display section will give certain video cards a considerable boost. With my GeForce Ti 4200 frame rate the frame rate increase was on the order of 50%. Not everyone will see that dramatic an effect but it's worth giving it a try.