For a higher-end system, the line out jacks are the better choice. Experiment for yourself and see which one works for your system. Microsoft, Intel, and others are working to improve the sound quality of PC speakers and sound hardware, with the goal of making PC sound rival that of home stereos. The USB ports promise to make connecting PC speakers a snap, in some cases eliminating the need for sound cards. And PC makers are phasing out the ISA bus in favor of PCI-based audio hardware.
Expansion buses make attaching peripherals and other components possible.
The industry standard is the ISA bus, the original 8-bit bus that appeared on the first IBM PCs. While ISA buses exist on just about every machine in existence, they are rapidly becoming obsolete in favor of two newer designs, PCI buses and AGP buses. You'll know when the brand new graphics card you bought requires a newer bus, and your machine sports only the old-fashioned ISA buses. Lots of peripheral owners find themselves with questions about their units, but can't make out the imprints and can't find their manuals. Peripheral cards are legally required to display a Federal Communications Commission ID number.