Undeveloped episodes during the run of the series
Boomers were originally to have featured more in the series' first season than they ultimately were; this was changed following the airing of the season's only Boomer-centric episode, "Fortunate Son". "We had another story or two planned with the Boomers," recalled series co-creator and executive producer Brannon Braga, "but we decided not to delve too much into meeting humans all the time." Reasons for this were that the writers wanted to avoid making it seem as if Enterprise was close to Earth and preferred to focus on other aspects of the Travis Mayweather character than his heritage as a Boomer. (Star Trek: Communicator issue 139, p. 24)
Jack Treviño, Steve Fratt and Dr. Joseph DiLella pitched several Enterprise stories, all serving what Treviño described as "lesser utilized characters" (i.e., Phlox, Hoshi Sato, Travis Mayweather and Malcolm Reed). One of these stories involved Phlox being compelled, by a powerful force, to create Frankenstein-type creatures out of six different species, including Humans. 
Pulp Fiction-like story
According to Linda Park in Star Trek: Communicator (issue 147), Connor Trinneer pitched a story similar to Pulp Fiction, told from the perspective of aliens. The Enterprise NX-01 crew would speak gibberish until they found a way to communicate.
Tan Ru story
The stories which Jack Treviño, Steve Fratt and Dr. Joseph DiLella pitched included one involving Tan Ru, the probe that went on to, as established in TOS: "The Changeling", collide and merge with Nomad. According to Treviño, at the time Enterprise was canceled, there was every indication that this story was about to be sold. 
William Shatner two-parter
One of these early concepts involved the mirror universe. At the Grand Slam XIII Star Trek convention in March 2005, executive producer Manny Coto recalled, "We had talked about doing a mirror universe episode ever since we got into Season 4. But then we had the possibility of getting William Shatner. Coincidentally, the Reeves-Stevens [Judith and Garfield Reeves-Stevens, who had worked with Shatner on several Star Trek novels] were a pair of writers whom I desperately wanted to bring on the show. And they, it turned out, had an idea for a mirror universe two-parter which would feature the return of William Shatner." wbm
At the same convention, Garfield Reeves-Stevens explained, "The idea was that the Tantalus field was not a disintegrator, it was a humane way of dealing with prisoners, by sending them back in time to a sealed penal colony. Enterprise (NX-01) comes upon the colony – and Tiberius [mirror-Kirk] is there. Tiberius thinks, 'Finally, a ship with a transporter – I can get back to my own universe, my own time.' He basically goes on the NX-01, gets to the transporter, sets it to go back to the mirror universe – the mirror universe doesn't exist." "It hasn't been created yet," Judith Reeves-Stevens added. Garfield continued, "So Tiberius and Archer work together to figure out where the division point is between the universes, what point that one split off into the other. And as it turns out, Tiberius and Archer together are responsible for the creation of the mirror universe." wbm
William Shatner himself pitched this story concept to executive producers Manny Coto, Brannon Braga and Rick Berman, over lunch. The idea was well received by Coto, Berman and Braga. However, Berman then pitched an alternative concept, this one having been devised by Mike Sussman. The idea was totally unrelated to the mirror universe and involved Shatner playing Enterprise's Chef, who Daniels would bring into the future to preserve the timeline by successfully posing as James T. Kirk during an important event in history. As Shatner and Paramount were unable to reach an agreement, the plans to have him included in the series were discarded. wbm However, the desire to visit the mirror universe remained, and resulted in the production of "In a Mirror, Darkly" and "In a Mirror, Darkly, Part II".
Colonel Green story
During the fourth season, Manny Coto wanted to do a story featuring Colonel Green (with Peter Weller as Green). In the words of Judith Reeves-Stevens, "It's lunch was eaten by the Soong," or, in other words, it became hard to do another story featuring genetically-engineered Humans. (The Augment trilogy was actually conceived with Green as their leader, but the character was instead made an ancestor of Noonien Soong to accommodate Brent Spiner's interest in appearing on the show.) Both Green and Weller were later seen in "Demons". ("Terra Prime" audio commentary)
One detail that would have featured in the episode was a flag first seen on Q's World War III uniform from "Encounter at Farpoint", which would have been tied to Green's faction. A flag featuring the emblem was produced for "In a Mirror, Darkly", with the hope that it could be reused, but this never came to pass. 
Mars independence story
During the fourth season, Manny Coto wanted to make an episode dealing with the Fundamental Declarations of the Martian colonies. The audio commentary for "Terra Prime" described it as a sort of Cuban Missile Crisis on Mars, with the comets used for terraforming the planet being aimed at Earth. The story never materialized, but the idea of comets being used for terraforming Mars found its way into "Demons".
In the special features for ENT Season 4 DVD, André Bormanis claimed that many ideas for Porthos episodes were pitched. These included Porthos becoming intelligent, Porthos being the only member of the crew capable of communicating with a canine alien, and even Porthos having to take command of the ship. Bormanis suggested that part of the reasoning why these stories weren't made was that the production staff didn't want Porthos stealing the show. Given the generally humorous tone of the segment, it might be that Bormanis was merely making these pitches up.
In addition, Breezy's handler claimed, in the segment, that he had suggested a story in which Porthos changes sex in a transporter accident, so to explain why the male Porthos was played by a female dog.
Proposed fifth season episodes
As Star Trek: Enterprise was officially canceled on 2 February 2005, its fifth season was never produced. The series' producers, however, had already devised plans for future seasons, which could have begun to air by September 2005. Most information is based on comments by producer Manny Coto.
At the 2009 VegasCon, Coto suggested that two story arcs of the season would have been to show "origins of the Federation" and "whispers of the Romulan war". Consequently, the Romulans would be the major villains of the season, although other species may have appeared in the mini-arcs. 
Brannon Braga also noted that he and Rick Berman had considered making "Future Guy" a Romulan. . However, later Braga claimed this was a red herring, and that the season would see future guy revealed as Archer himself, trying to influence his younger self to set right the timeline.  
Coto had also hoped that season 5 would see more stories offering social commentary, compared to season 4. 
Enterprise was due to revisit (or actually previsit) the cloud city Stratos on Ardana. In 2004, Manny Coto admitted, "I do want to do one or two episodes that take place on the Cloud City of Stratos. I want to see the early stages of that. I think it's a very fertile place for a storyline." (Star Trek Magazine issue 118, p. 23) Despite some initial ambivalence over whether he wanted the story to be comprised of one or two episodes, Manny Coto was later clearer about his intentions for the narrative's length when, in 2005, he spoke about how he regretted having been unable to fit the Stratos storyline into the fourth season. "I really wanted to do a two-parter on that location, to see Stratos in its earlier stages," he stated. "That was a wonderful location and wonderful setting for a great two-parter." wbm
A Kzinti episode had been suggested which would have served as a prequel to TAS: "The Slaver Weapon". The concept progressed as far as a "rough rendering" of a Kzinti starship which writer Jimmy Diggs commissioned. The story was provisionally titled "Kilkenny Cats." 
Mirror Universe story
Revisits to the mirror universe and Hoshi Sato, now Empress of the Terran Empire, had also been discussed. At the 2009 VegasCon, Coto revealed that one idea was to spread four or five episodes through the season, as a kind of "mini-series inside a series". He said that it was his "big regret" that he had not managed to follow through on the idea. 
Brannon Braga revealed via his Twitter account that before cancellation there was some talk about setting the entire fifth season in the mirror universe. 
Borg Queen origin story
Writer/producer Mike Sussman hoped to have T'Pol finally meet her father, and reveal to the audience that he was in fact a Romulan agent who had posed as a Vulcan officer prior to faking his own death. The suggestion that T'Pol was half-Romulan would have shed light on her affinity for Humans as well as her interest in experimenting with emotions. (, Information provided by Mike Sussman)
According to Entertainment Weekly, there was an episode "on the drawing board" to reportedly have featured Flint, under a previous alias, coming into contact with the crew of the Enterprise. The episode never made it to a script write, but initial storyboard ideas suggested a confirmation of Flint's alias of Abramson as a famous Earth scientist with possible connections to Flint knowing either (or both) Henry Archer and Zefram Cochrane. The episode would have ended with some type of discovery of Flint's nature by Phlox, leading to Flint's negative views on discussing his background with anyone, thus avoiding the "disaster of intervention" that he mentioned later in the TOS episode.
In a 2009 interview, British writer/producer Russell T Davies, showrunner of the British series Doctor Who, said that he had considered proposing a crossover between Doctor Who and Star Trek, but that the latter was canceled before the idea could be pursued.