The main changes that I know of are the following:
-sign painting (either removing both the English and Japanese, or occasionally translating Japanese)
-cultural references (the stereotypical rice ball)
-music (removes almost all of the original and replaces with new stuff)
-minor violence (guns are removed, either painted out or the scenes cut; physical strikes are replaced by impact stars)
-some sexuality (painting in swimsuit straps, lengthening Musashi/Jessie's skirt, REMOVING KOJIROU'S AWESOME CROSSDRESS COUGHCOUGH)
-cussing (but again, this is relative)
-inserting (and repeating) LOOOOOOOOTS of bad puns (Team Rocket's perpetual "that's SHOCKING" that has become as common as their motto? Yeah, NOT in the original)
Something people generally don't realize is also that, as in most 4Kids-cut anime, in the Pokemon dub, characters are not allowed to say "die" or "kill" or refer to God. Instead, stuff like "destroy" and "perish" as euphemisms... Also Mewtwo's inner conflicts about his creation and God in movie 1, for example, were removed... which totally changed the beautiful tone and story IMHO.
Also, movies are put in fullscreen rather than widescreen, so about a third of the image is cut off (a great example is in the Jirachi (?) movie, in which Gonbe/Munchlax is scratching of ticks and Haruka/May and Masato/Max are like "ewwww," but you can't see it because Gonbe is cut off in the dub.)