I found the following solution to this problem:
* BIOS -> PCI / Plug and Play Setup
 * Allocate IRQ to PCI VGA: Yes (before: No)

Kernels 3.2.0-39, 3.2.0-40, 3.5.0-26 work without problems. Kernel 
3.9.0-030900rc3 fails again in uvesafb, so I do not see anything during booting:
kernel: [    2.438172] uvesafb: Getting VBE info block failed (eax=0x4f00, 
err=0)
kernel: [    2.438222] uvesafb: vbe_init() failed with -22
kernel: [    2.438254] uvesafb: probe of uvesafb.0 failed with error -22

The Xorg.log is attached.

Some more information regarding my system:
* Mainboard: Elitegroup K7S5A
* BIOS: AMIBIOS 1.21.06
* Graphics card: GeForce FX 5200 in an AGP slot

While I can use the latest kernel without problems again, it would
probably still be interesting to find out the reason why I have to
change a BIOS setting with kernels younger than 3.2.0-38.

** Attachment added: "Xorg.log when booting 3.9.0-rc3 with 'Allocate IRQ to PCI 
VGA' set to 'Yes'"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1157878/+attachment/3643764/+files/3.9_rc3_Xorg.txt

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https://bugs.launchpad.net/bugs/1157878

Title:
  No X with nvidia after upgrade from 3.2.0-38 to 3.2.0-39

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