In Pacific Rim, the voice of GladOS from Portal can be heard (whether it was in the Gipsy Danger Jäger or the Hong Kong facility, I can't remember). Del Toro said he was a great fan and it was a wink to the video game.
In the Shape of Water, I'm almost certain I have recognized the voice of the Portal facility being used again as the voice of the Baltimore research facility. I don't think I have seen it confirmed anywhere (I haven't spent hours searching though).
Is there really no other connection to Portal than Del Toro being a fan? The repetition of this easter egg makes me thing there might be more to it.