I've a PSDME from SuperMicro: http://www.supermicro.com/products/motherboard/PD/E7230/PDSME.cfm

I can't use a PCI-card in the available slots, only the onboard (ATI) card.

See also this dutch topic for some logs: http://gathering.tweakers.net/forum/list_messages/1297558

The most important part is:
(II) PCI: 00:1f:3: chip 8086,27da card 15d9,9180 rev 01 class 0c,05,00 hdr 00
(WW) pciGenFindNext:  primary bus mismatch on PCI bridge 0x00010000 (0x01, 0x00)
(II) PCI: 01:00:0: chip 8086,0329 card 0000,0000 rev 09 class 06,04,00 hdr 81
(II) PCI: 01:00:1: chip 8086,0326 card 15d9,9180 rev 09 class 08,00,20 hdr 80
(WW) pciGenFindNext:  primary bus mismatch on PCI bridge 0x00010200 (0x01, 0x00)
(II) PCI: 01:00:2: chip 8086,032a card 0000,0000 rev 09 class 06,04,00 hdr 81
(II) PCI: 01:00:3: chip 8086,0327 card 15d9,9180 rev 09 class 08,00,20 hdr 80
(II) PCI: 12:00:0: chip 8086,108c card 15d9,108c rev 03 class 02,00,00 hdr 00
(II) PCI: 13:00:0: chip 8086,109a card 15d9,109a rev 00 class 02,00,00 hdr 00
(II) PCI: 14:04:0: chip 1002,515e card 15d9,9180 rev 02 class 03,00,00 hdr 00
(II) PCI: End of PCI scan
(II) Intel Bridge workaround enabled
(WW) Misconfigured PCI bridge 1:0:0 (1,0)
(WW) Misconfigured PCI bridge 1:0:2 (1,0)

The card is at 02:02.0:
01:00.0 PCI bridge: Intel Corporation 6700PXH PCI Express-to-PCI Bridge A (rev 09)
01:00.1 PIC: Intel Corporation 6700/6702PXH I/OxAPIC Interrupt Controller A (rev 09)
01:00.2 PCI bridge: Intel Corporation 6700PXH PCI Express-to-PCI Bridge B (rev 09)
01:00.3 PIC: Intel Corporation 6700PXH I/OxAPIC Interrupt Controller B (rev 09)
02:02.0 VGA compatible controller: nVidia Corporation NV34 [GeForce FX 5200] (rev ff) <--------- this one
12:00.0 Ethernet controller: Intel Corporation 82573E Gigabit Ethernet Controller (Copper) (rev 03)
13:00.0 Ethernet controller: Intel Corporation 82573L Gigabit Ethernet Controller
14:04.0 VGA compatible controller: ATI Technologies Inc ES1000 (rev 02)

This is the layout:
-[0000:00]-+-00.0  Intel Corporation E7230/3000/3010 Memory Controller Hub
           +-01.0-[0000:01-03]--+-[0000:02]---02.0  nVidia Corporation NV34 [GeForce FX 5200]
           |                    \-[0000:01]-+-00.0-[0000:00]--
           |                                +-00.1  Intel Corporation 6700/6702PXH I/OxAPIC Interrupt Controller A
           |                                +-00.2-[0000:00]--
           |                                \-00.3  Intel Corporation 6700PXH I/OxAPIC Interrupt Controller B


On the wiki i also found a page about 'PciRework', what is the status of this?

http://www.x.org/wiki/PciReworkProposal
http://www.x.org/wiki/PciReworkHowto