Mainboard (CPU Intel?) 2 * PCI-E x 16, 2-3 PCI, serial + parallel port

You could always get an add in board for parallel port and serial port.
Most boards have a SerialPort/COM1 dongle for the PCI expansion brackets. There are also USB adapters for both.

Pick the board you like, buy adapter, live happilly until next upgrade, take adapter with you to the next build.

Do you really need 2x x16 PCI-e , or will 2x x8 work? If so, check out the Gigabyte GA-P35-DS3P V2.0 if you can find one. There are headers for serial and parallel ports on the MB, so all you need are standard cable connectors to have the ports up and running.

PS - I may be wrong on this model -- it probably has 1x x16 and 1x x4 PCI-e slots.

Yes. You are right. It has 16x/4x.
I have a GA-P35-DS3P revision 1.0, it has both connectors on the back panel IO,
I also did not need 2 16x PCI-Express slots. Revision 1.1 is the same.
However revisons 2.0 and 2.1 DO NOT HAVE LPT/COM on the back panel.

I work with embedded hardware so both ports are a must have and I didn't want PCI expansion cards.

That's exactly why I picked the GA-P35-DS3P over P5K-E/WIFI.
A wifi card was cheaper than an LPT expansion card.

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Ya but these boards are dual card capable: says the specs. Most the boards I seen are 2x 16 are PCIe 2.0 and dont have parallel or serial. you cant have your cake and eat it to.

Gigabyte motherboards that have the LPT header have an unusual pinout. (Gigabyte provides the pinout on their website and in their user manuals.) The header is in a 2x13 configuration, which seems to be what is used on all motherboards that have LPT headers. Unfortunately, pin 24 rather than pin 26 in not connected, which is what makes Gigabyte LPT headers different. Pin 26 is connected to ground, but usually pin 24 would be connected to ground.

The DB-25 end of the LPT cable has 25 pins. Pins 18 - 25 should be connected to ground. If a straight ribbon cable is used to connect the LPT header (pins 1 - 25) to the DB-25 connector, then Gigabyte motherboards will leave DB-25 pin 25 unconnected (DB-25 pin 25 connects to LPT header pin 24).

Generic LPT port cables are available, and inexpensive. They use straight ribbon cables. They connect LPT header pins 1 - 25 to DB-25 connector pins 1 - 25 (but the pins are numbered differently).

Gigabyte has a LPT cable, part number 12CF1-1LP001-01R, but it is in fact just an overpriced generic cable. It uses a straight ribbon cable that does not compensate for the LPT header pin 24 vs. pin 26 issue.

If a circuit on a device connected to the DB-25 connector (via the Gigabyte LPT header and a generic cable) uses pin 25 for its ground connection alone, it will probably fail. If it ties at least one of the other DB-25 ground pins 18 - 24 to pin 25 (or doesn't use pin 25 at all) then it will probably work.

The Gigabyte LPT cable is not sold at many places, and they are overpriced and identical to the generic cables, which are cheaper and sold more places.

If you need a correct DB-25 LPT port from a Gigabyte motherboard, you could take a generic LPT cable, remove the ribbon cable from the IDC connector, split the ribbon between wires 23 and 24, twist wires 24 and 25 180 degrees, and reinsert the ribbon cable into the IDC connector: wires 1 - 23 where they were before and wire 25 where it was before, but put wire 24 at the end (where the 26th wire of a 26 wire ribbon cable would go), leaving a gap where wire 24 was.