We should compile a list of information regarding the use of this kind of converters. I'll start first...

Q: Is it safe to use the adapter with the "xyz" motherboard?
A: If you have the original AGP2PCI, then it is safe to use with any motherboard.
    If you have AGP.5 or AGP2PCIX, it is safe to use them with only 3.3v PCI signaling. Since PCI 2.1 manufacturers were recommended to implement 3.3v level. Since PCI 2.3 the manufacturers were required to use 3.3v signaling.
So: If you know for sure that your motherboard is PCI 2.3 or above compliant, then you are safe. If your motherboard has PCI-X slots keyed for 3.3v and want to use your adapter in one of them, then you are safe. If your motherboard is PCI2.1 or PCI 2.2 compliant and you clearly find in it's documentation that it is 3.3v PCI compatible, then you are safe.
EDITED:
Else, you have to test to see what level (3.3v or 5V) your motherboard uses. I will describe a very simple empirical test that has worked well for me. You need a multimeter. Connect the black probe to GND (black wire of a molex HDD plug is OK). Take a rigid thin conductor (a pin or a needle should do) and insert it in the hole corresponding to pin A17 of a PCI slot. Insert in that slot a PCI video card. Power ON the system. Go to BIOS. Measure the voltage between A17 PCI and GND. If you get close to 3.3v then you probably have a compatible motherboard with AGP5 and AGP2PCIX adapters, so you are safe. If you get close to 5v then sorry, but you have 5v only PCI, so don't use it with this type of converters.

Q: Why doesn't my AGP2PCI, AGP.5, AGP2PCIX work with my motherboard?
A: In a single word: IDSEL. IDSEL is a chip select type of signal used to configure the PCI bus. It is unique to every slot so the controller asserts IDSEL for slot "x" to talk to the device present in slot "x". It is implemented by using one AD line above AD[11]. The BIOS instructs what AD line is used for every PCI slot. On AGP cards, IDSEL is fixed to AD[16]. If the PCI slot that you are inserting the converter into uses AD[16] for IDSEL, then it will work. Else, you need to hack the BIOS of your motherboard to assign that value. Find the suitable BIOS editor program for your type of BIOS, open it and change Device Number for the PCI slot. Usually a value of 0 or 5 is needed for IDSEL=AD[16], depending on your motherboard implementation. I will not go more into it, as if you don't know what you are doing, then you really should not try it. Flash the modded BIOS. The selected PCI slot now should work with AGP to PCI adapters, but will not work any more with native PCI device unless you also do a hardware mod too. If however the desired to be used PCI slot and the motherboard's chipset sit on the same bus and the chipset already is setup to use AD16 for IDSEL (DEV 0) a BIOS hack might not help, as the chipset could be hardwired to DEV 0. The case where even if the PCI slot and the chipset are on the same bus, but still the BIOS hack will be effective is if the chipset has AD11 hardwired to DEV 0 (usualy the count starts with DEV 0 at the chipset from 11 or 16, there is no enforced rule).

More to follow...

Please post your experiences and tips too.

I stand corrected  I but doubt the meaning was lost due to my point omission

Please do, and get back with what you find.
For example, Tyan S2466 5V keyed slots use 3.3v signaling and BIOS hack works. MSI 6168 is 5v only.

Don't have to trust me, you can test yourself the MSI 6168 and see that it uses 5v signaling. Until PCI2.3 it was left up to the OEM how to implement logic level, AFAIK. A chipset might be both 3.3v and 5v compatible, but the motherboard builder was free to use one or the other (strapping configuration?).
Also, my memory might fail me, but I remember TNT2 is 5V tolerant. Go for Geforce2, that is a 3.3v only part in PCI.

Edit:
Oscar, do you have a MSI 6168? It would only take a couple of minutes to test it and confirm what voltage it uses for logic. Sure, it is not about this specific motherboard alone, but just to prove a point that better safe than sorry. A few minutes lost to test the motherboard, just to be sure nasty things will not happen

Loeschzwerg wrote on 11.12.13 at 19:42:52:


Thanks, Loeschzwerg! 
4v going straight through to a 3.3v only part. Sure it does work, we overvolt CPUs, GPUs and such all the time, but it exceeds certified limits. Not safe.
I warned above that measuring A6 is an empirical method, but good enough when access to professional tools is not possible.

Case 11 (Matrox G400 on AGP and VIA USB 2.0 on 5th PCI)
AGP: 3.8v on pin A6 (INTA like on PCI)
1st PCI: 3.8v on pin A6
2nd PCI: 5.1v on pin A6
3rd PCI: 5.1v on pin A6
4th PCI: 5.1v on pin A6
5th PCI: 3.8v on pin A6

Now... are you telling me I'm "overvolting" my G400 when it's @ AGP slot?!

Edit:
Case 12 (Radeon 9200se on AGP and VIA USB 2.0 on 5th PCI)
AGP: 4.0v on pin A6 (INTA like on PCI)
...

I will see if I can get an oscilloscope, everything else is not satisfying me.

No, you got it wrong what was said. It does not switch between 3.3 and 5. It is either one or the other. 5v card works with 3.3v motherbord no problem. Also, 3.3v card might work with 5v only pci,  just not safe. If a6 test is right, you have a 3.3v pci motherboard and 5v cards are opperated in 3.3v level logic, that is just fine and compatible. If a6 is not reliable test for logic level,  I will try to find other. I will play tomorow with an oscilloscope and report back here.

When I'm proven wrong about something I stated before, I'm not ashamed to admit that. A6 PCI measurement is not reliable, especially since it is an open drain signal connected to multiple slots. However, what was needed was a fail proof method and I think I've found one. I've edited the first post to reflect the following change:
Else, you have to test to see what level (3.3v or 5V) your motherboard uses. I will describe a very simple empirical test that has worked well for me. You need a multimeter. Connect the black probe to GND (black wire of a molex HDD plug is OK). Take a rigid thin conductor (a pin or a needle should do) and insert it in the hole corresponding to pin A17 of a PCI slot. Insert in that slot a PCI video card. Power ON the system. Go to BIOS. Measure the voltage between A17 PCI and GND. If you get close to 3.3v then you probably have a compatible motherboard with AGP5 and AGP2PCIX adapters, so you are safe. If you get close to 5v then sorry, but you have 5v only PCI, so don't use it with this type of converters.
The new pin to be measured is A17 . I have chosen it because it is an unidirectional signal, always from the motherboard (initiator) to the expansion card (target) and is unique to each physical slot. The signal on A17 is GNT#. As a proof that GNT# voltage is an indicator of the logic level in use, you can measure it on the AGP slot, where it is present on pin A8. Into an Universal AGP 2.0 slot insert a 1.5v only card and you will get close to 1.5v on A8. Insert a 3.3v only card and you will measure A8 at close to 3.3v.
In the light of this find, I tested 5v keyed slots on some motherboards and found that: Tyan S2466, Epox 8K3A, Biostar K8t890-A9 and MSI 6168 are 3.3v signaling compatible, so safe for AGP.5 and AGP2PCIX adapters use.