The older games' prices are affected differently when there is a re-release, compared to a sequel. As a relevant example with Pikmin 2, when re-released on the Wii, the Gamecube version went down slightly in value, since now it was available at a much cheaper price as a Nintendo Selects (and much easier to obtain). Now that Pikmin 3 sequel is out, people are nostalgic for the previous titles, and thus both Pikmin 2 on the GCN and Wii went up considerably in value (along with both original Pikmin versions).
For the Wind Waker HD re-release, since the price will be at the same or higher than you can get a used copy of the original, I don't know how much of an effect on its value the release will have. If anything the price will go down because people are more willing to sell their GCN copies when upgrading. The combo releases that you have are more immune to price drops, though, since they are much more of a collectable item than a cost effective way to play the games.
Not that I'm an expert on the subject, just my thoughts.
