Fundamental difference between OS X 10.6 Install Disc that come with New MacBooks one that comes in Retail Box-Pack
Retail discs are usually early releases (10.6.0 or 10.6.3) lacking driver support for newer hardware models.

Discs bundled with specific hardware models have full driver support and are usully more recent versions (10.6.5 or 10.6.6) but are also restricted to running on just that model or release series. They also contain install packages for any bundled applications such as iLife or iWork.

In most cases the retail disc should work and you should immediately apply the latest Combo update to add any missing drivers or feature support. If the retail disc gives you any errors you'll need the bundled disc.