What do you use your computer for? Unless you play games or use software that requires a lot of power (3D modeling like Solidworks, or rendering with Photoshop), upgrading probably isn't worth it.
About that stuff changing, that new PCI thing you mentioned is called PCI Express and it's aparently going to replace AGP. The change from AGP to PCI express will probably take years.
About that box thing. If it's just 1 PCI slot, it's probably not worth it. I have 2 sound cards in my computer so I can easily switch between headphones and the TV. RIght there I would have gone over the limit on PCI slots.
Try not to restrict yourself when it comes to expansions. Cheaping out will cost you a lot more in the end.