It all depends on what you want from your p/c, are you into games, video editing etc. If you do and can wait several months then it should be worth it. The biggest problem at the moment is that the benefits of PCI express will not be felt for least another 6- 8 months.
But if you buy a p/c that is equipped for PCI express then you have a head start and if you want to upgrade a graphics card you can.
All the articles I have read, every one suggests that performance levels should leave the 'old' AGP cards lagging well behind.