Storyline
One big difference in-between the manga and anime storyline is the fact that there is no Nehelenia sub-plot in the manga, as she is defeated for good at the end of the SuperS season there.
Instead of having Nehelenia as an added villain in the Stars arc, Naoko Takeuchi-sama created far more Anima Mates than ever get to appear in the anime. Anime Mates that never saw the light of day in the anime are: Sailor Metal Papillon, Sailor Lethe, Sailor Mnemosyne, Sailor Phi and Sailor Chi.
According to the anime, Sailor Galaxia was the strongest Sailor Senshi of them all, and destroyed Chaos by sealing it away in her body during the time of the Sailor Wars. Knowing that she would eventually be posessed by Chaos, the golden senshi herself sent her starseed off into the galaxy ("the lights of hope") so it could find someone that would eventually use it to defeat Chaos; this turned out to be Chibi Chibi.
Things are a bit different in the manga. In flashback scenes we see and learn that Galaxia was born alone "as trash" on a planet that was nothing but trash to her. Being a mere Senshi was not enough for her, as it equalled being trash as well. So she went in search of a planet that would suit her; a planet that held extraordinary power and would prove that she was better than ordinary senshi. But every planet she came upon seemed to be unworthy to her, making her destroy each planet while saying that it was trash. One day she stumbled upon Chaos who tells her that the Galaxy Cauldron is the place where all the stars of the universe are born. Galaxia wants this place to be her own; but to do that she needs the ultimate power of the universe and therefore starts "collecting" starseeds to gain exactly that power. Chibi-Chibi is also quite a different person in the manga. First of all, she actually speaks in full sentences in the manga (imagine that), and towards the end is shown to actually be Sailor Cosmos, the future and final (?) incarnation of Sailor Moon.
In the manga the Sol Senshi get killed off one after the other (first Jupiter and Mercury, then Venus and Mars, then Pluto and Saturn and finally Uranus and Neptune) leaving Usagi alone very soon (by the end of Volume 16!). Before the final fight with Galaxia, Sailor Moon even has to fight against her fellow senshi who have all been posessed by evil (and are all wearing Galaxia's bracelets).
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Personalities
The Sailor Moon manga is by far the more serious and not quite as lighthearted media of the two. This fact of course also reflects in the characters. There are still a few funny and cute panels, but they are very scarce and disappear almost completely with Volume 16 already.
Usagi is a much more mature character in the manga than she is in the anime. She's not as childish nor is she quite as ditzy and slow on grasping things at times. She is also by far more ready to fight; she was rather squeamish in the final battle in the anime, but this is - in my opinion - really not the case in the manga. Her powers are much more impressive in the manga, and towards the end, when she is indeed the last one standing, she is ready to sacrifice herself without a second thought.
Seiya is an alltogether different person in the manga. First of all Seiya is a fulltime girl in the manga, as she was originally intended to be and her character is very different from her anime self. She is a serious and actually rather quiet person, who never is obnoxious or big-headed or even arrogant. She is very focused on her mission, and never acts silly or carefree as she does in the anime. In the manga Seiya is sadly killed at Volume 17 and not among the last senshi standing as she is in the anime. After her starseed is taken we never actually see her or the other Lights again. ;_;
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