1. The Dauntless's quantum slipstream drive which the crew of Voyager copied.
2. The holographic equipment Reg Barclay created to send the Enterprise 30,000 light years to the center of the galaxy, which the Cytherians gave them the knowledge of but that Federation scholars would take decades to analyze (2399-2367 = 32 years have passed since then).
3. Kosinski and the Traveler's engine upgrades which sent the Enterprise 2,700,000 light years away.
4. Transwarp beaming/drive/conduits/etc.
5. Coaxial warp drive with the ability to fold space, which a Voyager shuttle was modified with so they had the technology.
1.) In my Head Cannon for the start of the 26th century, Quantum SlipStream drive is one of many "FTL options available".
2.) I'm not sure what happened in that ep, but something caused Reg Barclay to go back to normal intelligence and nobody followed up on trying to decode that tech?
3) The Traveler has abilities to make the Enterprise travel that far. Kosinski is a sham. And Wesley / The Traveler would just travel on their own personal StarShip or hitch a ride somewhere and go as far as they feel like. Eternal WanderLust.
4) Transwarp beaming - takes A BOAT load of Warp Core energy (Nearly all of it), just to send one person super far away. In the apocrypha, where they explained how Khan when to Qo'noS so fast, Khan had setup a series of Transwarp Transporter pads that were directly linked to the StarShips reactor. Every jump literally burned out the reactor of the StarShip it was on and would require extensive repairs. All this for 1 person to travel many light years to another pad until he reached Qo'noS. It's HIGHLY energy INefficient, HIGH energy consumption for moving 1 person, HIGHLY risky should there have been interference or something with the computer went wrong.
According to the novelization of Star Trek Into Darkness, beaming to Qo'noS for Khan was a more complicated plot. The small portable transwarp beaming device on the jumpship only had enough power to beam Khan to an automated cargo station on Earth's orbit. From there he accessed a heavy-load transporter to beam onto an unmanned vessel in orbit of Luna. Khan had equipped the ship with another unauthorized transwarp device wired into the empty ship’s engine. Utilizing the entire energy output of the engine for a single massive burst, he could have beamed anywhere in our galactic region. Transporting to Qo'noS completely burned out the device, so no one was able to follow him using it.
Basically, Transwarp across internstellar distances is generally avoided for the inherent danger, resource cost, and value proposition that it brings. Why move 1 person when you can move an entire StarShip there. Sending 1 person at extreme energy cost with no backup is fundamentally dumb, even if Khan was a Genetically Engineered Super Man.
Transwarp Drives = In my Head Cannon for the start of the 26th century, The Voth would have joined the UFP and come back home to Earth, sharing technology. Ergo sharing their technology and integrating it with the UFP.
Transwarp Conduits = In my Head Cannon for the start of the 26th century, StarFleet would have enough experience with Borg tech that they can manufacture their own Transwarp Conduits and it's the start of the next golden age for civilian travel between StarSystems and planets. Where your average civilians can take their "Space Cars" and literally drive between planets since they don't complicated engineering skills to maintain a complex reactor. Automated "Transwarp Conduits" literally create the equivalent of "Freeways" in space for average UFP citizen to travel about.
StarFleet StarShips of course can use this same method as well, but that's just one of many "FTL" options in their tool boxes.
5.) Coaxial Warp Drive - In my Head Cannon for the start of the 26th century, StarFleet reverse engineers the information on how it works from the data and modification specs of the Shuttle that were recorded during the trip. CoAxial Warp Drive is one of many "FTL" options in their tool boxes.
With the Various FTL drives on each StarFleet StarShip, certain drives would be faster than the other drives at a specific Warp Factor and be more energy efficient once you reach a specific Warp Factor. There would also be operating speed ranges for each drive and have Pro's/Con's for each.
I even added my own Next Generation "FTL" drive =D.