1. Ski-Jump on the trigger guard
2. Short magazine release
3. Lack of a weaver/picatinny rail
I believe the earlier production ones use a specialized rail system whereas later production models have a more standardized rail cut out on the bottom. Later production models also have an elongated magazine release which extends the magazine release almost an extra inch or something super groovy like that. IMO the elongated release is more desirable and easier to use.
edit: Looking at the photo there also appears to be a difference in slide serrations. The earlier ones were much more fine and greater in number. Later ones have fat serrations spaced further apart and have different rollmarking.
Wikipedia has a picture they claim to be a "Gen 1" P99. Compare it to a modern production found on the Walther site.