So I was on a windy island and took some 20k+ shots in total, as I expected, many sequences have little shakiness from the strong wind, it`s not a lot but enough to notice. I tried to do the “foto stack” in Photoshop but it takes some time to do a sequences of 300 – 900 pictures at a time. The other option I have is to do it with After Effects, just wondering which gives the better results or are there other options specialized on this?

BTW, I did all with an old Canon 30D which I was not using anymore, I almost wanted to give it away at some point. Not sure how others cameras perform, I know my new Sony A77 can make about 400 pictures (at most!) with one battery charge, this old Canon still with the original battery takes easily 6000+ images with one charge.

After Effects Warp Stabilizer is usually the way to go.

I use wrap stabilizer in Premiere Pro and it works great on fixed shots. I am trying on an Hyeperlapse sequence and the results are more mixed.