1) The plot in manga runs significantly faster then the anime. Some parts of Episode 3, 7, and 8 of the anime does not exist at all on the manga. For example, unlike episode 8 in the anime, there is no Misaki vs. Misaki fight in the manga.
2) The relationship between Icchan and Ogata is a little bit different in the manga. In the manga, rather than playing "Ogata Torture Games", Icchan will just simply tell Ogata "to die" or "I will kill you" if he fails a job. There is no "Live Octopus for ten minutes" in the manga :-).
3) In the anime, I do not recall Misaki directly/indirectly referring Hikaru (her angel) to Hikaru (in Magic Knights Rayearth). However in the manga, there is literally a scene that shows Misaki is daydreaming about making Hikaru into a character of a certain manga she read before, and the back of Hikaru (MKR) is also explicitly shown in the manga.
4) In the manga, the faces of the other Angelic Layer competitors (like Sai) are not shown when they are "scouting" Misaki. This is not true in the anime.
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