Re: Star Trek Into Darkness out on Blu-ray/DVD September 10th [spoiler
A question from an aspect ratio n00b.
It was my understanding that filmmaker always shot in widescreen because you got more of the picture that way. Every TV however used a 4:3 ratio and I heard people complain all the time about movies shot in widescreen being altered to fit 4:3 in full.
Actually, filmmakers shot/shoot with different aspect ratios in mind for the final product. Without getting overly technical (as I don't have time at the moment), the standard ratio until the early 50s was 4:3 ish (1.37:1 vs. the 1.33:1 of a standard TV). Films with that aspect ratio fit perfectly well on SDTV screens. In the 50s, wide screen ratios (varying from 1.66:1 to 2.70:1--think Ben-Hur) were introduced to compete with TV. There had been a few widescreen films earlier, but they were quite rare.
By the 1970s, two widescreen ratios had become the norm (though others still popped up as well): 1.85:1 (which on HDTVs leaves very tiny black bars top and bottom because HDTVs are 1.78:1) and 2.35-.40:1 (those leave black bars top and bottom on HDTVs, though not as thick as on SDTVs).
Why is is now that we actually have HD TV's that are also by design wider that we still get films with the black bars?
Answered above.
Is is just a choice? Certain films are shot wide but in full frame and they look fabulous? Is now just simply a visual preference?
Choice of aspect ratio is an artistic decision by the filmmakers. Studios (with exceptions to very influential filmmakers) reserve the right to modify the ratios for home video releases (though since HDTVs became common, they have not done this too much) and for broadcasters/cable channels. In those cases (think HBO and Cinemax and so on), many 2.35:1 films are "zoomed" to fill the 1.78:1 (16x9) HDTV screen. It seems people tolerate "black bars" when movies are rented on discs, but not on cable channels.

Movies with a 1.85:1 ratio are often "zoomed" to 1.78:1, both on disc and on TV channels, but the effect is extremely minimal. With wider ratios, the effect can get quite ugly, though not as bad as the pan and scan days of VHS.
If it is, as a director if I knew we were shooting a variety of scenes in IMAX I would also choose to film the rest of the movie in a similar fashion so as to avoid the Dark Knigh Blu-Ray fiasco.
Ah. Here is where I disagree. I found the "fiasco" quite satisfying as it highlights the IMAX imagery, just as it did in the cinema. I will concede that the effect probably works better on home cinemas with projectors (as I have) than on a 40" HDTV in one's living room. That's why I think a shifting ratio should be available, but would prefer it not be the only option. Warner's should have released the Batman films with branched chapters to give those with smaller screens (and those who prefer a fixed ratio) a hi-def option.