I'm a system builder, have been for about 8 years now.
To echo the others, yes its not really any cheaper to build your own any more. Although it still can be in the long run.
Branded pc's STILL use legacy hardware that are extremely specific/fussy to their own brand and what hardware they use.
I've had about 6 people in the past year ask me to upgrade the memory om their PC World bought rigs, only to find that high quality ram like Corsair XMS won't work in their stupid system, even though its the same running spec. Go to PC World and its literally 4x the price i get better ram for.
Had a couple wanting to game on their rigs. But can't fit a decent gfx card in cos the case is either matx and clustered up to hell or something else sits in the way preventing a full length card going in.
The bios tend to be locked so you cannot tinker with it for overclocking reasons etc. Overclocking a system can be breathe new life into an older rig that has fallen behind the times as far as speed goes, thus saving money on buying newer faster parts etc.
Overall, if you have the knowledge its still far better to build your own from individually purchased parts.
Half of the warranty's offered by brands are crap anyway. You get a problem you return the pc, they spend time looking at it, leaving you without a pc. If it were your own built one, you'd most likely have the knowledge to identify the issue, RMA the part, but have the option to buy a replacement part (better than buying a new pc) in the interim.
Just my 2 penneth.