Centering (or adding black bars)

Is there a way to center the video in the available space so that there are equally sized bars on the top and bottom?
If you are using QT Pro to combine your files into a single large clip, simply use the built-in adjustments:
1) Open the "Properties" window.
2) Select the video track whose display you wish to adjust.
3) Select the "Visual Settings" tab at the top of the lower half of the "Properties" window.
4) Enter your "Offset" adjustments as desired. The normal algorithm here is expressed as

Offset = (b-a)/2

where "b" is the width or height dimension of your display screen and "a" is the width or height dimension of the content you wish to center along the desired axis within the display.
5) Save the modifications using the "Save" or "Save As..." option or export to re-compress if desired/required.

Alternately, is there a way to actually add black bars to the smaller clips so that they're all the same height?
Since the background is, by default, black, adjusting the "smaller" clips in the manner described will "letterbox" or "pillar" the content automatically. If a black, other color, or custom frame background is desired/required for the largest clip, you can create it in a graphic application like Photoshop, scale it to the length of your final "combined" file and adjust offsets as desired for the video content. Also consider that "centering" is but a single option here. You could, for instance, create a double width player and center your video content on one half of the player and add text comments, annotations, captions lyrics, etc. centered/displayed in the other half of your enlarged display area.