Generally the X server driving the AGP card has to be started first.
AGP sever restart leads to system crashes. In gdm.conf, set AlwaysRestartServer=false.
The new X server patch (XFree-4.3-prefbusid) fixes most of the problems.
The first and the last combination are reported to work without major problems with XFree86-prefbusid.
Nvidia GeForce4MX440(AGP)+TNT2M64(PCI)+TNT2M64(PCI)
Matrox MGAG400(AGP)+Matrox MGA1064SG[Mystique]PCI
Matrox MGAG550DH(AGP)+Riva TNTM64(PCI)
Matrox MGAG550DH(AGP)+Geforce4 420(PCI)