Compiled from personal observation along with this post and the responses to it. I am now convinced that this fandom has the best ship names ever. All the ships that involve the Avengers plus Loki and Coulson: 

• Tony/Steve: Super Husbands, Stony, Starkers, Stark and Stripes
• Tony/Bruce: Science Boyfriends/Husbands, Rage Against the Machine, Stanner, Brony, Trucey, Science Bros (platonic), Science Alliance (platonic)
• Tony/Thor: Iron Thunder, Thunderiron
• Thor/Loki: Thunderfrost, Thorki
• Tony/Loki: Ironfrost, Frostiron, Starki
• Coulson/Loki: Frosted Doughnut, Iced Coffee, Coulki
• Bruce/Loki: Gammafrost, Green-Eyed Monster 
• Natasha/Loki: Black Ice, Black Frost
• Clint/Loki: Frosthawk, Snowbird
• Steve/Loki: Ice Frost, Frostshield, Capslok
• Bruce/Clint: Hulkeye, Angry Birds, Green Arrow?
• Bruce/Thor: Thunder Science, Gamma Hammer
• Steve/Bruce: Spangled Banner
• Steve/Thor: Captain Hammer, Captain Thor, American Thunder, Thundershield 
• Steve/Clint: Captain Hawk, American Eagle?
• Natasha/Clint: Black Eye, Blackhawk, Clintasha
• Natasha/Steve: Cap Widow, Cap Tasha, The Cold War, Stasha
• Natasha/Tony: Iron Widow
• Natasha/Thor: Thortasha, Black Thunder?
• Natasha/Coulson: Coulwhip, Black Tie
• Natasha/Bruce: Black Hulk
• Thor/Clint: Thunderbird?
• Tony/Clint: Ironhawk, Hawkiron
• Coulson/Steve: Capsicoul 
• Coulson/Clint: Shield Husbands, Bowtie, Phlint
• Coulson/Tony: Iron Agent, Iron Taser 
• Coulson/Thor, Coulson/Bruce: ?
• Natasha/Coulson/Clint: Agent Clintasha
• Tony/Steve/Bruce: Stark Spangled Banner
• Bruce/Loki/Thor: Super Smash Brothers
• Bruce/Tony/Loki: Gammafrostiron
• Bruce/Tony/Clint: Technobow
• Tony/Loki/Clint: Iron Hawk of Mischief 

Other: 

• Pepper/Tony: Pepperoni, Pepperony
• Bruce/Pepper: Green Pepper, Dr. Pepper
• Bruce/Pepper/Tony: Dr. Pepperony
• Pepper/Steve/Tony: Pepperstony, American Pepperoni, Stark Spangled Day Planner
• Pepper/Tony/Loki: Peppertoki, Frosted Pepperoni
• Natasha/Pepper: Red Pepper, Black Pepper
• Natasha/Maria: SHIELD Wives
• Bucky/Natasha: Winter Widow
• Bucky/Steve: Starbucks, Winter Shield?
• Tony/Jarvis: Cyber Husbands
• Tony/Rhodey: Iron Husbands
• Tony/Howard/Steve: Starks and Stripes
• Bucky/Steve/Tony: Frosted Winter Shield 
• Thor/Jane: Fosterson, Thane
• Loki/Jane: Lokane
• Loki/Darcy: Tasertricks, Larcy
• Bruce/Darcy: Electric Green
• Steve/Darcy: Shieldshock
• Clint/Darcy: ShockArrow
• Fandral/Darcy: Fancy
• Steve/Sif: Warshield 
• Johann/Loki: HYDRAFrost
• Johann/Bucky: Jokky
• Johann/Loki/Bucky: Jolocky

Know of any I missed?