Different heads have a different combustion chamber size (usually measured in cc's) and that will affect your compression ratio (and hence, whether you can use regular gas or if you're forced to use methanol, etc.).
Most small blocks can swap heads and intake manifolds. Beware that 400's use heads that have special steam holes in them to accomodate their siamese cylinder cooling system. Swapping other SBC heads onto a 400 without drilling these holes will cause it to immediately overheat.
Also, the smaller motors (305, for instance) had heads that don't flow very well and, while they will bolt up to a larger small block, will choke the hell out of a larger motor.
In '96 GM switched to their "Vortec" series of motors and made a bunch of improvements, for instance better (reusable) intake and valve covers gaskets. The cylinder heads were also more efficient and made much better power than their predecessors. Any motor that uses the vortec heads requires a vortec specific intake manifold along with centerbolt valve covers (which began in the late 80's, again because they seal much better than the previous design).
The LT and LS series motors are a whole different deal, but I assume that's not what we're talking about here.
Ok, ultimately, tell us what motor you have and what you're thinking about doing with it
