The differences i encountered so far:
MSI has 2x8 pin (Gigabyte 1.0 1x8 + 1x6 pin, Gigabyte 2.0 2x8 pin)
Gigabyte is longer due to cooling system (might fight tighly in smaller cases)
Gigabyte has revised cooling, powering the core with 8 phases wheres MSI is 6 phase (greater has better stability)
Gigabyte has white connectors wheres MSI has blue (female DVI)