One of the first peeks I got from the actual filming of Episode 1 was a report about Liam Neeson being filmed in a swamp area, which turned out to be Qui-Gon and Obi-Wan escaping the tanks on Naboo. When I've read the report though, I always envisioned that swamp as dark and moody as Dagobah was... probably at night, blueish lighting, a lot of fog. Well, it turned out to be a rather lush green and sunny scene...

Actually I think since Lucas always stated that the prequels were going to be darker than the OT, "Empire" and especially the Dagobah sequences were what I've based my basic expectations for the prequels on in terms of atmosphere. Several dark and very moody paintings by Ralph McQuarrie (especially of Imperial City on Coruscant) supported this... and even now, when looking at McQuarrie's concept art, I wish that was how the prequels looked.