Marvel
Incredible Hulk #1
Bruce Banner turning into the Hulk. I think that's also Betty and General Ross on the cover.

 

Spoiler

Click to see actual cover

Winners:

• Aernaroth (Publisher)
• Aernaroth (Series)
• None (Issue)
• Aernaroth (Characters)

 

DC Comics
Elseworld's Finest - Supergirl & Batgirl

 

The Mighty Thor, published by Marvel, that's the aforementioned Thor and Hercules, I don't know the issue number.

 

I know you know, but just being a stickler and fair. I'm assuming that's just the title guess and you forgot to include the series/characters. (even though the title gives the other answers away)

 

Ah yes, the characters are Supergirl and Batgirl. Series - Elseworld's (or Elseworld's Finest?)

 

Spoiler

Click to see actual cover

Winners:

• Dead Metal (Publisher)
• MTME (Series)
• Dead Metal (Issue)
• None (Character)
• Dead Metal (Homage)

 

Spawn?

 

Yup, Spawn #227 homaging Amazing Spider-Man #300.
Published by Image comics.

 

Hint: Variant

Spoiler

Click to see actual cover

Winners:

• ABH1979 (Publisher)
• ABH1979 (Series)
• ABH1979 (Issue)
• ABH1979 (Characters)
• MTME (Homage)

 

Looks like princes purple rain cover

 

Hint: Graphic Novel

Spoiler

Click to see actual cover

Winners:

• Sinestro (Publisher)
• Sinestro (Series)
• Sinestro (Title)
• Sinestro (Characters)

 

Yup, that's what they were going for.

DC
Batgirl
#40 Cliff Chiang variant (which is actually the second time he did this homage with Batgirl)
Batgirl and Batman

 

Marvel
Captain Marvel
The Death of Captain Marvel
Captain Marvel, Spider-Man, Hulk, Captain America, The Thing, Dr Strange, Thor, Colossus, Iron Man, Daredevil, Wolverine and Death.

 

Spoiler

Click to see actual cover

Winners:

• None (Publisher)
• MTME (Series)
• None (Issue)
• MTME (Character)

 

Batman beyond
Batman

 

Spoiler

Click to see actual cover

Winners:

• Dead Metal (Publisher)
• Dead Metal (Series)
• Dead Metal (Issue)
• None (Characters)
• None (Combination)

 

Spider-Boy #1
Amalgam Comics (Marvel and DC)
Spider-Boy and two villains, the ice Carnage guy and a lizard thing. No idea what they're called again. Just knew it was this because I used tk have the issue.

 

Added a new section to the last round. Since we already know it's an Amalgam comic, see if you can figure out who the new character(s) are a combination of.

 

Spoiler

Click to see actual cover

Winners:

• iamste (Publisher)
• iamste (Series)
• iamste (Issue)
• iamste (Characters)
• iamste (Homage)