To name a favourite from the stories / comics it is hard to tell. I probably have most of the EQ material here but from that I'd say original quest series (I read them first as a translated and colorized version). Some HY parts (Rayek's story), EQ Vol 2, Worldpool, Kahvi, Wavedancers...
Original quest, well, it had grip and bite, it was my first EQ experience and I knew the characters then. The others brought a lot of new characters and sometimes I lost overview.
Admitted I often did not have the time to read them in one block like I did back with original quest.
Same problem with the new Final Quest. It comes shipped by tfaw but the releases are 3 months apart. So I could just re-start reading from the beginning every time. :/
Concerning the characters, well, it's obvious, right? (If it is not: "jaRf" stands for "just another Rayek fan".) So favourite character is Rayek. For a lot of reasons.
But there are a lot of other characters I like, and Elfquest has a lot of characters.
Venka and Clearbrook, my calm and soothing ladies. Redlance and Teir for being calm / mysterious and calm. Maybe Skywise. Tyleet, Ekuar to name some more.
There are even characters I don't like but I see them as necessary addition to the story.