• you have the advantage of decent public transit it EU, take advantage of it – in the US, most often we simply don’t have the time to take “slower” options (we can go across the country in a few hours by plane or three long days by train – EDIt: or a grueling week long challenge on bus)
• prioritize your options, rank them by something like “level of guilt” and “level of tiredness” (in addition to “cost”, “convenience”, “availability”, “bike facilities”) – ex. trains get preference, planes are left for when you’re too exhausted to even think of anything else
• plan circular routes / loops / circuits rather than a there-and-back approach – you’re now facing “the last leg” or “closing the loop” rather than just figuring out how you’re getting home from some singular destination

This is a complex question with no easy solution that makes sense for everyone. A few notes from my personal perspective on it:

• What you do in terms of everyday life is where the greatest focus should be in terms of carbon footprint and what not. As an example, let's say you drive, and decide to go someplace 500 km away on vacation. You think wow, a 1000 km round-trip is a lot. But if you're putting 20K km/year mileage on the car just commuting, running errands around town, etc. that's what really adds up for most people.
• If your vacation has an element of visiting family or friends, just do whatever it takes. Life is short.
• Hauling a bike around over different modes of transport sounds like a giant hassle. Is there any way to rent one at the destination? Failing that, maybe something like a small folding escooter might travel better?

I'm planning to fly transcontinental once every 8 years for the rest of my life, but I'm being pretty strict with myself for anything shorter than that and going train or bus. For me it's not exactly about the personal impact as much as doing it to make it easier for others in the future to do better. So every time I "suffer" a little because I take an extra day to travel by train/bus, I just think about how my doing it makes it more likely that train service with bikes will get easier for the next person to do the same thing. (Also I live in the US so most routes are much much harder than pretty much anywhere in Europe from what I hear.)

Are you really cycling far enough to warrant a flight? Is it about the journey or the destination? I would think you don’t do that kind of distance without loving the journey to the point of trivializing the destination. So for a given trip, you could just as well cut the outbound trip in half. It need not be a back and forth trip as the redundancy is what you want to avoid. So make it a triangular route.

Whatever your distaste is for buses, perhaps that can be remedied with small mid-trip stretches. Find a city pair where the journey is overall uphill, then book a bus just for a short segment of your trip. You get a more interesting window view for an hour or two than you would in a plane, and a moment to rest between cycling segments. You can do the same with ferries.

It’s also surprising to hear that you find it easier to take a bicycle on a plane than a train or bus. The fee for that must be small on buses and trains than on a plane. And hard to trust airline baggage handlers with your bicycle.

Might be worth looking into taking a blabla car, though it might be hard to find a ride who can spare the space for a bike.

In some South Europen countries you find these dodgy small private bus tour organizers who carry (ex-)emigrants and their families to and fro. They tour to one or several places in Northern Europe with a small bus and trailer on a somewhat regular schedule, and you can probably fit your bike in the trailer, for less than the price of an air ticket. Can probably found on facebook or by asking in the local cafe of wherever your bike has carried you to.

Happy biking!

And to answer your question, do I ever take a flight. This is the first year I've really considered not flying and will probably opt for a bus. I just fly to visit my family and wouldn't really do it for anything else, but even that felt wrong given that other options exist. I'd love to be able to take a train, but I can both not afford the money it costs and the time it takes. I only have a couple of weeks off.

The flight will happen with or without you..... they won't be gassing the plane up just to take you to and from, so I don't see why hitching a ride on something that's already going that way would be terrible