Here's my list:
1. Ripto(pretty much the only recurring villain in the series, and I like recurring villains

2. Red(I just always thought he was cool. Plus, Mecha-Red was epic)
3. The Sorceress(this witch is just pure heartless. Who could even THINK of murdering 151 cute and innocent baby dragons JUST FOR THEIR WINGS?!)
4. Gnasty Gnorc(Gnasty was too generic for me. But, gotta remember: He was the first villain in the series

5. Grendor(UUUURGH. I never liked this guy. Maybe it's just me, but I think he's too bland)
Notice that I didn't include The Sorcer(e/o)r, Cynder, Gaul or Malefor because I haven't played Shadow Legacy or The LoS series.