Well, every amp will color the sound. You just can't get around that, really. It starts with trying to amplify the acoustic to begin with, and our ears try to find a 'sweet spot' of an electrical manipulation of what we think an acoustic should sound like. It's an audio cup and ball game in a sense.:-) But I think the Baggs amp is the best so far in regards to that question. Their Ibeam and M1 setup is pretty darn good all things considered, in an acoustic environment.
I like the kind "amps" that involve a mic and mixing board ;)
but, i have a K&K mini w/ vintage jack in my Collings D1A from there I usually go into a LR BAGGS DI dox and then to the board (i usually do this as a safety backup in case the sound guy is paying attention to his beer more than the band and I can mix myself from the stage).
Bob's right, about acoustic amps. they all sound strange to me if that is your only source. the Bose system ROCKS! I have to say I'd own one right now it they weren't $2,700. but they sound great from small venues.
The reason AMPS sound strange to me is because you're "hearing" sound that has been hyped by the amp makers to mimic the sound you naturally hear coming OUT of your guitar - and that sound has some serious spectral energy - it full and rich and abundant in overtones, transients, etc...YUMMY! the tone you get from the amp is a bad photocpoy of that (remember the 10th generation xeroxes you had to read from in high school chemistry class?) ok it'snot that bad...but sort of..
There is a cute little 100 watt amp that is extremely clean and uncoloured. It is marketed by AAD and is called the Cub. It weighs practically nothing and comes with a cool little carrying bag. Perfect little thing for flying.
It ain't cheap, but it is good.