What are some cheap, reliable methods of water-proofing switches and buttons?
For waterproofness you can't beat.


Magnet + reed switch 
Magnet + Hall sensor.


Reed switch has advantage of zero off power and no lower voltage limit.

Hall sensor can be more robust.
 Reed can be extremely robust if mounted well (floating in soft packing)

These BU520xx hall sensors from ROHM cost about $1.20/1 from Digikey BUT have under 10 uA off state current drain worst case.
 2.4 - 3.3 V operation.
 If current does not matter you can get 6 MA when off parts for about 1/2 that cost.

If you want single cell operation at 55 uA typical for a horrendous $9.72/1 you can have this marvel.
 NVL AFE series. Operation down to 0.9V.