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Here are what Selenium IDE says about those two commands :
click(locator)
Arguments:
- locator : an element locator
Clicks on a link, button, checkbox or radio button. If the click action causes a new page to load (like a link usually does), call waitForPageToLoad.
And :
clickAt(locator, coordString)
Arguments:
- locator : an element locator
- coordString : specifies the x,y position (i.e. - 10,20) of the mouse event relative to the element returned by the locator.
Clicks on a link, button, checkbox or radio button. If the click action causes a new page to load (like a link usually does), call waitForPageToLoad.
click is used when you just want to "click" on an element, like a button, a link, ...
And clickAt is used when you want to "click" on a position designated by mouse coordinates.
I suppose the second one can be useful for some "rich" applications -- I've actually never used it... On the other hand, I use click like all the time.
If you have a page with form elements, links, buttons, and stuff like that, you'll probably generally use click : it's way easier to find an element using it's id or classname than having to find it's position in pixels on the page ^^