Off shelf- vs custom built computer

Off shelf advantages
Relatively cheap
All in one package
No assembly required
Warranty intact
"Boot and it works"
Disadvantages
Integrated Sound
Integrated video
Integrated parts, if they break, computer is screwed
Non-replaceable components

Custom Built?
Cheaper!
Custom selected components
More bang for the buck in terms of raw power
Open Source OS
Fully custom tweaked to your preferences

Disadvantages?
No warranty (you must fix it if something goes wrong)
Potential for fake parts during purchase
Chance of hardware failure increases with user idiocy (where applicable)
Open Source OS (unfamiliar work environment)
Different software set (basic tools, word processors, etc)