You've got a lot of properties listed here, so for the sake of clarification, let's break them out.
The Marvel Cinematic Universe (MCU) is where the films produced by Marvel Entertainment / Disney take place. This includes current films Iron Man (1, 2, 3), Captain America, Thor (1, 2), The Avengers, and the Hulk film starring actor Ed Norton, as well as several smaller films which are distributed with these films (the Phil Coulson shorts, the one with the Chitauri item, and the Mandarin short). Upcoming films for this universe include, but are not limited to, Guardians of the Galaxy, Avengers 2, Captain America 2, and Ant-Man. Marvel's Agents of S.H.I.E.L.D. television series is also considered a direct part of this universe. The MCU properties will interact with each other, but will likely not interact with anything else. Marvel Entertainment may license Marvel to produce comics explicitly set in the MCU, such as a prequel or side-story; these comics will state such a fact, but based on observations of other such products in the past, it is unlikely media external to the films/television show will be referenced by the films/television show.
The Marvel Comics Universe (MU) is where all of the standard Marvel comics take place. It has versions of everyone and even added a Phil Coulson analogue. It has crossed over into the Ultimates Comic Universe through cross-dimensional portals. Notably, its version of S.H.I.E.L.D. with Maria Hill, is used in the Marvel Cinematic Universe.
The Ultimate Marvel Comic Universe (UU) is a "hard core" version of the standard Marvel Comics, and their premiere super team, The Ultimates, is the inspiration for at least the Samuel Jackson iteration of Nick Fury and some concepts used in the Cinematic Avengers. It has crossed into the standard Marvel comics universe through cross-dimensional portals. You may be misuing the term "The Ultimates", which refers to the Avengers team as they exist within the UUC. It is not a term used elsewhere in any of the other universes.
The Ultimate Avengers animated universe from the "Ultimate Avengers" cartoon series featured a version of The Avengers which followed the story set by the Avengers of the Marvel Cinematic Universe, but was cancelled when Disney acquired Marvel Comics. It had not, and likely will not ever be due to its nature, be referenced in the films.
The Avengers Assemble animated universe is comprised of the "Ultimate Spider-Man", "Avengers Assemble", and "Hulk: Agents of S.M.A.S.H." animated cartoons, all taking place in a separate animated Marvel universe which is based on the Marvel Cinematic Universe, even referring to The Chitauri aliens from The Avengers, but as these cartoons have an inherent silly nature to them and diverge from the film universe, they will likely will not be acknowledged within the context of the films.
The Amazing Spider-Man Cinematic Universe is from Sony and features Andrew Garfield as Amazing Spider-Man (Amazing Spider-Man 1, 2) has not crossed into any other properties.
The Spider-Man Cinematic Universe is also from Sony and features Toby MacGuire as Spider-Man (Spider-Man 1, 2, 3) had a spin-off cartoon on MTV called "Spider-Man: The New Animated Series", which followed the trilogy film storyline. It was not referred to by the film series.
The X-Men Cinematic Universe is from FOX and features the X-Men (1, 2, 3, and First Class) and Wolverine films (1, 2) references its own films, and will likely explain where each sits during X-Men First Class, but otherwise has not crossed into any other properties.
Other Properties: The Ghost Rider, Fantastic Four, Blade, Daredevil (and Elektra) and other Marvel film properties are stand-alone except where their own sequels are concerned. Blade: the series television show attempts to extend the Blade cinematic timeline.
There may exist "easter eggs" in some properties, most especially sourcing from the comics and cartoon properties, extending into the other properties for one-off encounters, but these incidents would likely not ever be acknowledged canonically by the receiving properties.