You should always use a tripod to avoid parallax errors (ghosting). Even 
then, it will sometimes shift slightly after adjusting it so images are 
sometimes misaligned by one or a few pixels. You can often get away with 
shifting (translating) them in Photoshop or similar but Hugin will usually 
do a better job. You should limit optimizations to Yaw, Pitch, Roll.

I got the same idea back in 2007 when panorama-documenting an old power 
plant. It was a huge project and I ended up with a huge pile of over 60.000 
images that's still far from finished post-processing. I spent a year 
writing a personal tool ("PicStack") from scratch in C, which identifies 
and merges similar images and finds the best placement automatically. I 
also added a set of color adjustment functions and automatic HDR merging 
with diffuse masks generated dynamically but then Enfuse was released and 
it was superior for that so I don't use that feature much anymore. The main 
purpose of Enfuse is not stacking similarly-exposed images but it does work 
for that as well. I personally consider that a "bonus" though and still 
prefer using my own tool for that to know what I get and then if I need 
exposure fusion I'll pass my output through Enfuse in the end. I intended 
to release my tool to the public but as it's always been "in development" I 
didn't get that far. The parameters to differentiate likely HDR-intended 
shots from non-HDR especially needed endless tweaking.

I usually took 4-5 identical images, sometimes more, and it really saved my 
neck as you can squeeze lots more dynamic range and shadow detail out of a 
cheap camera's JPEGs. There were cases when I retained grey levels from the 
pitch black corners where pixels only consisted of noise flipping binary 
between 0 / 1! By doing a radical gamma curve adjustment to bring up the 
light before merging, you can regain lost detail almost as if by magic if 
you have enough shots.

I used this tool for all the panorama material below. (Sorry for 
self-promotion) :-)
http://www.angkraftverket.se/datidnutidframtid/merainfo.html

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