The difference can be as simple as some performance enhancements, or as huge as support for more memory, faster processors, better capacitors, more ports (internal and external), support for multiple graphics cards, etc.
You are asking a very broad question. Comparing two specific boards would yield much better answers.
That's why, when building a system, you don't just get the best board available, you get the one that fits your needs. Too many people ask others for advice on this, instead of realizing no one else can answer this but them.