To add my 2 penneth.
I am in the fortunate position of having driven a 993, 3.4 996 and facelift boxster (as well as my current GT3) and the 993 is old technology in terms of the drive and interior. The 996 is light years ahead of the 993. The 993 was 10yr old design when it was launched and the 996 was introduced to bring the 911 into this century. Don't believe all the hype, air-cooled engines had their fair share of problems also - there is a very good reason why no manufacturers continue to use air cooling. I'm not saying the 993 is a bad car, it isn't, but it is old technology and very much feels it.
In terms of boxster vs 996 - the boxster is a far better b-road drive, more fun, balanced, pointy. The 996 is a sporty GT - better on the motorways and long drives. The boxster is more practical (more boot space). So depends on what you are wanting really. If I wasn't tracking a car I would be back in a boxster in a flash - screw all the pillocks that say "couldn't afford a 911" - they've obviously never lived with both cars, but at the end of the day your insides need the 911 badge then a 996 would be the way to go - great car, but for the same money a much younger boxster S would be my choice.
Remember Porsche admitted that it costs them the same to build a boxster and a 996 - and they were definitely making profit on the boxster, so that tells you a lot. Apart from the GT2/GT3 or TT (where the engine alone cost £28K) it is the only porsche where you are truly getting value for money.