For one, with the CPU speed, you are going off the old "clock speed is everything" adage which is no longer true unless you compare a CPU to another within it's group. The Intel Pentium Duals and Core2's where faster than AMD's Turion X2's clock for clock, so in this case the Intel based Vaio is probably pretty even with the Gateway in terms of performance.
The only things going things going for the Gateway are the larger HDD and the cheaper price, but the fact that it is a refurb is usually a turn off to many.
Neither system uses a dedicated graphics card, so don't expect any miracles there. Both have 2gb of RAM which is pretty much the sweet spot for Vista nowadays.