If you need MODIS satellite data, you should check Nasa’s Reverb web portal. It is a, and I quote, “next generation metadata and service discovery tool”. But, as it turns out, is is already available for our generation ;-), just head over to http://reverb.echo.nasa.gov/.
It has indeed a fairly convenient interface in the form of an online map. You just zoom in to the area of interest and than click and drag a bounding rectangle.
But there is another option, which I hadn’t seen before. Not sure it is a new option or I have just overlooked it all the other times. You can upload a shapefile marking your area of interest.
It will than find all tiles (they call in granules) that fall within your polygon and produce a list with download links. Note that the shapefile can have 50 vertices (points connecting the lines). No problem if the shapefile contains more, but it will be simplified automatically, so check if the end-result is still OK.
Assuming you have selected the data you need (in my case that was the MYD14A2 fire data layers), you can following the next two steps (self explanatory) after which you will be given a download link for a text file that contains the download links for all the selected tiles.
You can than use data transfer tools like wget or cURL to batch download the data. For example, if you are using linux, you can simply use:
> wget -i <url text file>
This is a very convenient way to download large number of files in batch. You really got to appreciate how the NASA not only makes all this data available, but also makes a real attempt to make it as easy as possible.
In case you need more guidance in how to use this tool, they also provide a tutorial.