Thank you, b0uncer. Removing the case cover was only a kind of emergency procedure, because 95C (65C when idle) is too hot. The design of the cover is optimized only for the CPU fan and the CPU isn't getting much hotter (keeps at ~30C).
Using nvclock I've found that AGP was disabled, so I've changed the option "NvAGP" in the nvidia driver configuration from "1" (use nvidia's AGP driver) to "3" (try first to use the driver in the kernel). Things are a little better. FPS in Flightgear reached two digits

and glxgears now runs 7x faster, making 70 FPS (~90FPS when the system is idle)... Of course, things are still wrong. Still with the case opened and without external fan, the temperature is 57C when idle and 79C when gaming.
These are the relevant parts of my xorg.conf:
Section "Module"
Load "i2c"
Load "bitmap"
Load "ddc"
Load "extmod"
Load "freetype"
Load "glx"
Load "int10"
Load "type1"
Load "vbe"
EndSection
(...)
Section "Monitor"
Identifier "L1753T"
Option "DPMS"
EndSection
Section "Device"
Identifier "NVIDIA Corporation NV34 [GeForce FX 5500]"
Driver "nvidia"
EndSection
Section "Screen"
Identifier "Default Screen"
Device "NVIDIA Corporation NV34 [GeForce FX 5500]"
Monitor "L1753T"
DefaultDepth 24
Option "NvAgp" "3"
Option "ConnectedMonitor" "DFP"
SubSection "Display"
Depth 1
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
SubSection "Display"
Depth 4
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
SubSection "Display"
Depth 8
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
SubSection "Display"
Depth 15
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
SubSection "Display"
Depth 16
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
SubSection "Display"
Depth 24
Modes "1280x1024" "1024x768" "800x600" "720x400" "640x480"
EndSubSection
EndSection
The card name is obviously wrong, but AFAIK this doesn't matter.
Thank you again