For me, these were the advantages, but they may have changed nowadays:
1. Customize everything, including case
2. Usually cheaper (my old build was $200-300 less, but that may have changed nowadays)
3. If you don't want an OS, you don't pay for one (I already had a copy of XP, so I didn't have to pay $100 more)
I think the higher price the model, the less it makes sense to customize. If your budget is around $500-1000, customization is the way to go.