The Windows Experience Index tests the performance of the processor, memory, graphics chip (both general and gaming/3D), and the primary hard disk. Since the WEI tests only tests specific components, and not how they interact with one another, the figures are not a good indication for how well a system works for your usage pattern.
In Windows 7, the ranges of the scores have been extended, from 1.0-5.9 in Vista, to 1.0-7.9 in Windows 7. This extension has been introduced due to the improvements made in various hardware components. Microsoft also fine-tuned the scoring rules, and this tuning is what makes the scores differ between Vista and Windows 7.
A common component to see a drop in rating is the primary hard drive. Based information gathered through performance feedback loops, Microsoft found that a lot of disk drives seem to suffer from a problem where continuous small write operations seriously clogged the drive in question, seriously hurting responsiveness of Windows. Unfortunately, this problem appears to be rather common, with early solid state drives leading the pack. To take this common problem into account, Windows 7's WEI recognises the problematic drives, and caps their scores. In other words, if your hard drive score dropped between Vista and Windows 7, you might simply have a crappy drive.
At the danger of starting a nerd d*ck-waving competition, here are my scores for my two Windows 7 machines. My desktop:
My Aspire One netbook has the following scores under Windows 7: