I'm in the process of restoring a Motorola MEK-6800-D2 evaluation kit.
 The kit was adapted and has its RAM on a separate board through an
 EXORciser backplane.
 After putting everything together and verifying that all looks good,
 I've applied +5V from an ATX power supply.  The '-' prompt appeared, the
 JBUG monitor program is working and I even dumped the ROM and some
 EPROMs over the cassette port and decoded them on a PC :)
 So far so good, but to do anything cool I need the RAM board going.  The
 problem is that this (custom wire-wrapped board) is using 16 MCM4116
 chips. They need also -5V and +12V. Ok, these are available on the ATX
 power supply but I'm affraid of doing anything stupid that might blow up
 something.
 What would you check before applying these additional power levels ?
 I've been verifying a bit with an ohm meter that the -5V and +12V leads
 are not by accident connected to anything they shouldn't but not sure if
 that's a good way. 
Thats a good start :-)
I would certainly power up the RAM board on its own, without the
processor board connected. Then check that none of the bus lines have
+12V or -5V on them.
You mention that the memory board is wire-wrapped. I assume, therefore,
the ICs are socketed. I micht well m,ake a layout diagram, remove the lot
(or at least anything that's hard to get or expesnice), power up, and
make darn sure no pins are at +12V or -5V that shouldn't be. This has the
bonus that you'll reseat the ICs when you put them back, possibly
eliminating socket problems for the moment.
 I also read in the datasheet that you need to apply -5V before the
 others and removing it after the others. How would you do that ? I was
 thinking on having the -5V and GND permanently connected. So after
 switching on the power supply it will have -5V right away. Then manually
 connect a additional cable having GND, +5V and +12V.  On power off do
 the reverse. Is that a good idea ? Not very handy but if it works I'll
 live with it. 
Normally, the difference in loads on the supplies (-5V being very lightly
loaded) means that the -5V line comes up first if you just supply them
all from the same PSU. Not having an ATX PSU, I cna't be sure it'll
behave in thsi way, but the older PC/XT and PC/AT supplies should do,
3-rail DRAMs were used in some PC add-ons. I've worked on plenty of
machines with 3-rail DRAMs and seen any more elaborate power sequencing
than simply the difference in loads.
-tony