These series still feel too different to really compare and contrast, but I'll just go ahead and describe what I liked about each series.
Out of these three, I'd probably go with American Dragon as my favorite. I liked the idea of dragons being able to have a human form. Not really a new idea by any means, but it was kind of cool all the same. Though, I think that I liked this show the most out of the three mainly for the second season. The first season was okay, although Jake was speaking in slang talk way too much and most of the episodes that weren't connected to the Huntsclan/Rose plot were kind of dull from what I remember. The second season brought better character designs for most of the main cast, the episodes were much more interesting, the development for the Jake/Rose romance was pretty nice and I think that the Homecoming episode was the only time I cried while watching a Disney Channel Original Series.
I still wish that the show got a third season, or at the very least a longer finale since the ending for the series, while still pretty good, was seriously rushed. I also remember liking Jake's friends. They were kind of fun and I liked that they were actually helpful, instead of going through the usual keeping the magical world secret from non-magical beings. I think that I would have had Jake's Dad learn about the Magical World either after he stood up to those vampires or after Jake went back in time and his father helped him out. I think it would have meant more in either case than in the finale since that was where his Dad was at his best for me.
Danny Phantom would be second for me. I thought it was a fun show with fairly likable characters and a nice premise. I never thought it was too funny and inconsistencies in the characterization in later seasons was kind of annoying. The special episodes were usually pretty good and I thought that the finale was pretty satisfying, except for Tucker being the mayor for some odd reason.
The Life and Times of Juniper Lee would be my least favorite out of the three. I could never really get into the series. It had a nice premise, but I couldn't get attached to the character. Juniper's little brother was kind of annoying and I didn't really like that she couldn't tell her friends about her role protecting the magical world or even leave her city. That just seemed a bit too much. Plus, I didn't like that the characters looked and acted older than elementary school students. For some reason, that tends to annoy me with some shows.