There is not an explicit setting for changing the background color of the line number column (Eclipse Helios, SR2, Build id: 20110218-0911). However, there are work-arounds and here is one:
The line number background changes color according to any changes you make in the Text Editors "Background color" - so the two are the same. Between these two is the column holding the debugging breakpoints (not sure what that column is called) and it's background color is not affected when changing the general background.
I run Eclipse on Linux (Oracle's version) and access it with XMing X-server from a PC. Setting this background color to a very pale yellow makes the narrow column holding the debugging breakpoints standout - and that column is between the text and the line number column. So the effect is to make the boundaries of the line number column more clear.
The very pale yellow is #FCFFC8 = RGB 252,255,200 = HSV 63,22,100
Eclipse often behaves a little differently when I run it straight from my PC so this behavior may be one of those cases.
Hope this helps.