Thanks for remembering Major Bludd's name! I forgot what it was, because when I was little my friends and I used to give him the codename "Scorpion", so I always thought of him as that.
Regarding which comics I recommend, here is a list of the story arcs from both Marvel and Devil's Due comics' G.I. Joe series that I found to be the most memorable:
From the original Marvel Comics Series:
1. The Very First Issue. Where General Hawk shows the 'Joes their new base, the Pit, and Cobra Commander and the Baroness take over an old spanish fort, holding a bunch of people for ransom. This leads up to an interesting second issue, where the 'Joe team must protect the Alaskan pipeline from being sabotaged by Cobra. These first story arcs were what started it all! As a kid, I used to re-enact this story with my G.I. Joe toys. I even built the spanish fort using building blocks and legos; this brings back some memories.
The second issue was where we learn that Snake Eyes' face is messed up. A commanding officer orders him to put his mask on in order to make himself presentable. It would be a long time in the series, before we could see why.
2. The Takeover of Springfield. This was Cobra's attempt to contol an entire American town as a show of what it could do. Destro's first appearance was about at this time, as was the HISS tank. Cobra used a lot of brainwashing on the people of Springfield, and the takeover was gradual and insidious. It became unofficially known to the fans as "Cobra Town", and it served as a base of sorts for them until Cobra Island showed up in one of the later issues.
It was interesting how, no matter how hard the 'Joes tried to root Cobra out of the town, they just couldn't becuase so many people were Cobra agents, yet sometimes themselves never realized it. Talk about a truly sneaky plot!
3. The Silent Snake Eyes Issue! You weren't a real fan of the 'Joe comics if you didn't real this one. Not one word was spoken in the whole issue. Not a single thought bubble either. The whole thing was a silent drama as Snake Eyes fought Storm Shadow and an enemy Ninja clan. This was when Scarlett first became attracted to Snake Eyes, and her face conveyed the emotion a lot better than words could have. Snake Eyes kicked major butt in this story! I called this one the Silent Ninjas issue, and it had a lot of serious Ninja butt kicking action in it. It is probably one of the best Snake Eyes stories *ever*.
4. Cobra's Civil War. This was in the later issues. Doctor Mindbender created Serpentor to replace Cobra Commander, who was in hiding at the time. But, unexpectedly, Cobra Commander snuck back and took control of the faction of Cobra that was still loyal to him. They prevailed, and he ended up sealing away the traitors in an old abandoned shipwreck on Cobra Island. Even the Baroness wasn't safe, and Destro for a while was ready to go against Cobra Commander to save her. This story arc had a huge amount of intrigue, and marked the first time when Cobra actually killed their own, for their cause. Up until the Red Shadows arc in the DDP series years later, this was considered by many to be the darkest chapter in the history of the G.I. Joe Marvel run.
5. The Crimson Guard. Way before the Cobra Civil War, the Crimson Guard were introduced. These were ordinary people involved in corporate business who joined this elite group, gave up their real names, and became known as "Fred" and then a number. Such as "Fred III", for example. At this time, Cobra Commander's son Billy surfaced and an attempt was made on CC's life. CC then went to extremes to get revenge on those responsible, and this led to constant paranoia amidst those loyal to him over those who were not. All of this intrigue was the first sign of what would lead to the Cobra Civil War, and a good use forshadowing of future events and their dire consequences.
6. The Origin of Snake Eyes. This issue really was interesting! It told about the time when Snake Eyes was serving in Viet Nam and his face got hit by a hail of gunfire. Later on, it was revealed that he also suffered severe burns from a different incident not related to his time in the Viet Nam war. This was the first time that G.I. Joe talked about a real war, and the trauma caused by that war. It was hinted at, that Snake Eyes had some kind of a serious emotional problem because of being in 'Nam, and Scarlett's feelings for him became even stronger. I think it began, for her, as genuine pity for Snake Eyes, and it was from there that things grew. This was actually a sad story. One moving sequence showed Storm Shadow in Viet Nam trying to rescue the injured Snake Eyes amidst almost impossible odds. The end of the story explained that Snake Eyes' loved ones were killed in a car explosion that was tied to the machinations of the man who would become Cobra Commander.
It was also revealed that a large factor in Snake Eyes' disfigurement was a helicopter explosion which also left him unable to speak save for rare times.
7. Snake Eyes gets Plastic Surgery. After the Cobra Civil War, the 'Joe team had some down time while Cobra re-organized itself. While Rock 'n Roll was showing the 'Joe teams new base to some kids who wanted a tour, Snake Eyes and Scarlett decided to see about Snake Eyes getting his face repaired.
In this story, we learn that attempts were made before... and that Snake's face, although hideously scarred, was once much worse than it is now. The doctor thinks he can repair Snake Eyes' face, and conducts the surgery. As Snake Eyes is totally sedated and entering his recovery from the operation, the Baroness shows up, kidnaps Scarlett, and almost kills her at one point in this story arc. Snake Eyes rescues Scarlett, and the Baroness has to leave to bail Destro out of his latest trouble with Cobra Commander, which is a lot.
8. The 'Joes go to Canada. I have no idea why I remember this story as vivid as I do, it wasn't even that good. A small team of 'Joes team up with some Canadian Mounties to help solve a murder investigation which soon turns out to have been partly the work of a bear and partly the work of terrorists who they have to uncover and bring to justice. This was a boring story, though, and I don't remember more about it other than this, since around the time I first read it, I discovered Frank Miller's The Dark Knight Returns graphic novel. Needless to say, my attention shifted to Frank Miller's legendary masterpiece.
9. The Introduction of Zartan. This was memorable because it was a very big let down for me. The actions figure of Zartan was cool, and I thought that in the comics he would be an interesting villain. Instead, he was the leader of a biker gang and just seemed to be hired by Cobra to commit petty vandalism to distract people from Cobra's real doings in the areas where the vandalism was taking place. This wasn't long after Destro's introduction into the series, and it just felt like a cheap way to introduce another new character too soon afer already introducing a very cool character indeed (Destro). Ironically, I recall the issue before it saying - "Next Issue: The Dreadnoks!" and since it was before the Dreadnoks figures came out, I wondered what a Dreadnok is. I thought they were going to be fearsome creatures or Cobra war machines, and in the end they were just Zartan's biker gang, a bunch of petty criminals. It wasn't until much later in the comics that Zartan became a more cool type of villain, and he and his sister Zarana kind of grew on me over the years.
10. The G.I. Joe Team is Disbanded. I remember this issue, and how in it the big ceremony came where the team was told to call it quits. Snake eyes was going to marry Scarlett and it was implied that Flint and Lady Jaye were also about to settle down. The Pit was closed, and Cobra was no longer going to be considered a threat that required the 'Joe team's services to fight against.
From the DDP (Devil's Due Press) G.I. Joe Comics Series...
1. The Red Shadows. This was one nasty story arc. Lady Jaye is killed by a mysterious organization that is trying to eliminate both G.I. Joe and Cobra so they can unleash a deadly doomsday plot involving military weapons arrays that can target key locations around the globe. Flint goes off in search of revenge for Lady Jaye's death, Cobra as an organization just about falls to pieces, and in the end the leader of the Red Shadows escapes while Flint is left to cope with his wife's death and the fact that he cannot avenge her. This was, perhaps the darkest chapter in the history of the 'Joe team, since the Red Shadows (unlike Cobra) were far more concerned with causing chaos and death than they were with actually fighting for a specific cause at all.
2. Hawk is Shot. This happened not long before the Red Shadows story arc. During a mission against Cobra, Hawk and Cobra Commander get into a big fight. Cobra Commander shoots him in the back, only to himself be shot by the Baroness, who takes off with Destro to sieze total control of Cobra. Hawk is hospitalized and has strange dreams and learns that he is paralyzed. The Baroness is also having odd dreams because all of the brainwashing Cobra Commander gave her is wearing off. She finds out she's pregnant by Destro. Eventually, Cobra Commander recovers and General Phillip Rey replaces Hawk as the leader of G.I. Joe, leading into the Red Shadows story arc, in which it is discovered that in fact it was Zartan, disguised as CC, who was shot.
I stopped reading G.I. Joe comics when the Red Shadows storyline finished, so I don't know anything about the issues following that. Also, forgive any inaccuracies in my synopses, since I am just going by memory alone here.