I don't see this project as being massively difficult, as long as you don't expect it to be entirely self-powered, with a display, for 100 years:
# Low power RTCC chip for timekeeping, or ridiculously low power MCU on its own. Flash retention issue solved by self-reprogramming the MCU 'periodically' (every 10 years).
http://ww1.microchip.com/downloads/en/DeviceDoc/20005010F.pdf achieves <1uA and has leap-year compensation built in to year 2399.
# Crystal accuracy can be improved by calibrating for precise frequency during manufacture, and temperature compensating during use. Use redundant oscillators and RTCCs if you're paranoid, at the expense of power consumption.
# Energy harvesting power source - the key is to power it from as many sources as possible. Mains power + Lithium battery + solar cells, thermocouples, microphone, piezo, coil antenna, wind-up mechanism, whatever etc, all charging a supercap for powering the RTCC. We must be able to get a few microwatts out of the air somewhere. Oversize the supercap and battery to allow for degradation. LT make some energy harvesting stuff:
http://www.linear.com/parametric/energy_harvesting# "Mains Power" means 3-30V AC/DC - who knows what sort of voltages will be around in 100 years, but it's a safe bet we'll be able to feed this thing with 12V from somewhere, somehow. Since this is the only direct electrical interface to the outside world, protect it heavily with TVSes and redundant polyswitches.
# Use whatever display you like, but only light it up when it's powered from the mains. Gives incentive for customer to mains power it thereby increasing the time the unit is powered from a reliable source. LED is probably the best lifetime - they reduce in brightness, but never 'die' unless you overdrive them. Mains power also charges internal lithium battery and supercap.
# Make a mould, and pot the whole thing under light vacuum in a cube of transparent ('optically clear') polyurethane resin. Sort of like this (but use good resin)
http://www.ebay.com/itm/EPOXY-RESIN-CRYSTAL-CLEAR-CASTING-IMBEDDING-1-5-GAL-KIT-/220350141369. Use IP-rated vandal-resistant switches for setting the countdown time, or use capacitive or optical sensing only when mains power is present or there's significant charge in the battery. Potting will help prevent the supercaps drying out and make it "infinitely" rugged (no tin whiskers, moisture ingress, corrosion, or susceptibility to mechanical damage to worry about). Transparent shows off the internal construction, and you don't need to worry about holes to see the display through.
Not a trivial project, but I don't think it's beyond the realms of the hobbyist with today's technology. Nuclear power sources notwithstanding.