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 the films Iron Man (1, 2, 3), Captain America (1, 2, 3), Thor (1, 2, 3), The Avengers (1, 2), The Guardians of the Galaxy, Ant-Man, and The Incredible Hulk (starring Ed Norton, but not necessarily The Hulk starring Eric Bana). This also includes several smaller films distributed with these films (the Phil Coulson shorts, the one with the Chitauri item, and the Mandarin short). The TV series Marvel's Agents of S.H.I.E.L.D. and the Netflix series Daredevil and Jessica Jones are also considered in-continuity for the universe. There are additional in-continuity films and Netflix/TV shows announced, but it is not worth listing them until they are released.
These 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 this as matter of fact, but based on observations of other such products in the past, it is unlikely that any media created external to the films/television productions will be referenced by the films/television productions.
The Marvel Comics Universe (MU) is where all 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 established by the Avengers of the Marvel Cinematic Universe, but was cancelled when Disney acquired Marvel Comics. It had not, and likely will not ever due to its nature, be referenced in the films.
The Avengers Assemble animated universe is comprised of the Ultimate Spider-Man and spin-offs, Avengers Assemble, and Hulk: Agents of S.M.A.S.H. animated cartoons with an inherent silly nature to them; these all take place in a separate animated Marvel universe based on, but distinct from, the Marvel Cinematic Universe, even referring to The Chitauri aliens from The Avengers, but using identical characters in notably different ways. For example, the teenage Luke Cage from Ultimate Spider-Man is distinctly not the same iteration of Luke Cage from MCU's Jessica Jones.
The Amazing Spider-Man Cinematic Universe from Sony featuring Andrew Garfield in The Amazing Spider-Man (1, 2) has not crossed into any other properties.
The Spider-Man Cinematic Universe from Sony featuring Toby MacGuire in Spider-Man (1, 2, 3) had a spin-off cartoon on MTV, Spider-Man: The New Animated Series, which followed the trilogy film storyline. It was never referred to by the film series.
Notably, a deal has been struck between Sony and Marvel/Disney that a third iteration of Spider-Man, distinct from the prior 2 Sony versions, will appear in one of the upcoming Marvel Entertainment films (purportedly Captain America 3: Civil War), and will also have his own film.
The X-Men Cinematic Universe from FOX features the X-Men (1, 2, 3, First Class, Days of Future Past, Apocalypse), Wolverine (1, 2), and Deadpool films, which reference each other, but otherwise never crossed into other properties.
Additional Independent Properties: The Ghost Rider (1, 2), Fantastic Four (Corman, 1, 2, 2015), Blade, Daredevil (film starring Ben Affleck), and Elektra and other Marvel film properties not mentioned here are stand-alone except where their own sequels are concerned. Blade: the Series television show extends 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.
Not, have there been crossovers with the MCU? Not officially in the sense that it would ever be addressed in the MCU. Most "crossovers" are with the MU or UU characters (who interacted a lot, especially during the 2015 Secret Wars), but notably Spder-Man had a Spider-Verse crossover where he met every significant iteration of Spider-Man, including film and cartoon versions. This would never be acknowledged on film, and none of the Spider-Men he met were the MCU Spider-Man.