The Dragon #1: Start of an extended version of the original SD miniseries.
Savage Dragon #76: Dragon awakes in a completely different universe.
Savage Dragon #145: Start of the "Back in Blue" arc. SD #145-169 form possibly the most epic era of Dragon.
Savage Dragon #170: With Dragon apparently dead, Malcolm and Angel take center stage.
Savage Dragon #193: As a tribute to Captain America #193 marking the return of Jack kirby to that character, SD #193 marks the official beginning of Malcolm's tenure as the series' main character.
Best Single Issue Reads:
Hard to pick any single issues of SD that jump out individually, but I do have a soft spot for Savage Dragon #188.
The Dragon #1-5: Extended version of the original miniseries, introduces Dragon and sets up his world.
Gang War (Savage Dragon #24-26): With the death of head baddie OverLord, the super-powered gangs of Chicago are at war.
A Talk with God (Savage Dragon #27-33): Witness the birth of Dragon's son Malcolm, the death and ressurection of Dragon himself, and guest appearances by the Maxx, WildStar, Spawn, and even God and the Devil.
Savage She-Dragon (Savage Dragon #51-58): WIth Dragon dead again, She-Dragon takes the lead.
End of the World (Savage Dragon #73-75): By the time this storyline ends, nothing will ever be the same again.
Image World Tour (Savage Dragon #132-144): In Dragon's search for his missing wife, he encounters Spawn, Invincible, Witchblade, Bomb Queen, and other Image characters.
Savage Dragon #0: The origin of Dragon. Probably best read around SD #150 (which included this story as a back-up).
Emperor Dragon (SD #145-169): Possibly the greatest storyline in all of Dragon's history. What happens when the ghosts of Dragon's fogotten origin come back to haunt him and his friends?
Savage Dragon on Trial (SD #184-192): After the events of the Emperor Dragon arc, Dragon returns home to Earth, alive and well. But not everyone is welcome to see him again.