I notice that Andy and I pretty much use many similar methods, and I'm with him. I don't want to boil my tomatoes too much, so when I have to peel and seed, I used the time-honored method of slicing a shallow cross in the bottom end and immersing in boiling water for a very little time, then in ice water and peel. Seeding is a pain, but I also slice the tomato vertically, then stick my thumbs in and push the seeds out. I do that first, then put them through a food mill if I want it to be more carefully seeded.
If you are mostly growing (or buying) fresh tomatoes for sauces, be it canning or freezing, it helps to grow (or buy) a variety that is best for that. I'm sure others might know more but Italian plum tomatoes and last year I grew Amish paste tomatoes. These have a higher "meat to seed" ratio in my experience. Personally, I only do preserving of tomatoes that are in excess of those I eat fresh, and prefer the more acid-y taste for fresh eating.
Boiling a tomato for a longer period of time than it takes to loosen the skin can actually defeat your purpose: the "meat" of the tomato can get mushy and make it harder to remove the seeds without sacrificing the rest of the tomato.