I've had an issue for sometime regarding 4 blank icons that I couldn't remove from the Springboard. I would do the usual delete process but after a respring or reooot, they would reappear! The icons themselves are web links, not required for any of the applications which I have installed.

Went on Apple iPhone School website and found a fix for the above issue:

[Only registered and activated users can see links. ]

So, my Springboard looked like this with the blank icons:

I went into my iPhone via SSH, went to var/mobile/Library/WebClips and there were 4 folders for the blank icons:

I deleted these 4 folders and then resprung the Springboard and the icons were gone:

I believe some themes may put blank icons on to the Springboard so you can use this method to get rid of them.