In addition to the memory (and slowness) problem, this question combines two other issues that I've thought about before. The problems only arise _if the gif files are animations_, but the solution could be similar:

 1. [When importing GIF animation, how to find the correct list of “DisplayDurations”?][1]
 2. [Does Mathematica support variable frame rate for any video format, in analogue of GIF-style “DisplayDurations”?][2]

In the second post, I answered my own question by writing an export function that assembles the movie from a sequence of frames, _but outside of Mathematica_. This by itself could already help with the memory problem:

**Assuming you're on Mac OS X** and you manage to get all the frames into a Mathematica list called `images`, you could use the function `exportMov` I defined in [my answer][3]

 exportMov["video.mov", images]

On that page I also have a link to a Python utility that can be used to achieve the same thing from the command line completely without Mathematica and relying only on built in Mac OS X functionality - but that's off-topic for this forum. 

If you want to use an external tool, you may want to look at [this page where I describe how to use `convert`][4].

**Edit**

One more thing that could make or break any attempt to even import the images into Mathematica is this (your question already does this, but I think it bears repeating): _Always_ end your `Import` statement with a semicolon to suppress the display of the image frames. Otherwise, with a large number of images, the notebook interface will be busy drawing them for what feels like an eternity.


 [1]: https://mathematica.stackexchange.com/q/5361/245
 [2]: https://mathematica.stackexchange.com/q/4727/245
 [3]: https://mathematica.stackexchange.com/a/4903/245
 [4]: http://pages.uoregon.edu/noeckel/MakeMovie.html