My favorite arcs are the 1st, 2nd, 3rd (because of Orube), 5th and 6th.
The 1st is so mystical and iconic. It's so interesting to get to know the
Metamoor, Elyon's and Rudolph's past and see the W.i.t.c.h. girls' different reactions after finding out they're guardians. Overall I love the moments of any magical girls learning to use their new powers! And Cornelia's grief when Elyon got lost was so heart-breaking

I adore their friendship so much!
The 2nd one is creepy and I love it. Nerissa's own haunting melody and the previous guardians are interesting! Also I like Cassidy's death because it gives some perspective on how dangerous and evil Nerissa is, and it feels dramatic because in magical girls comics characters don't die so often.
I like the 3rd arc because Orube is one of my favorite characters and she has both funny and adorable moments in earth. Also Taranee was such a boss in the arc.

This was the first arc (with the 6th one) I read because in Finland they re-published the arcs 1-3 with omnibus editions and the first comic book I got as a kid was the book with the comics in the middle of the 3rd arc. I still remember it was a warm summer day I rode to a shop with my bicycle and got the book
The 5th arc felt so special to me because I love books, and the whole plot about the magical book, people being trapped inside of the book and all of the riddles were so interesting! And all of the hypnotic powers near the element rocks (or whatever they've called in English) were so cool since I go crazy with any plot with hypnosis
I grew up with the 6th arc. The W.i.t.c.h. comics were published in the Finnish W.i.t.c.h. magazines (1 comic in a magazine) and my first W.i.t.c.h. magazine was near the beginning of the 6th arc. (So simultaneously with reading the 6th arc I read the re-published omnibus editions of the 3rd arc). The ragorlang monsters were actually very scary and the whole plot of an old evil woman stealing teenagers' lifes creeped me out.