I was wondering what every ones opinion was on connecting the fan directly to power supply or using the mobo headers. I understand I have more control over speed and such but is it harder on the board ?
Its no harder on the board as long as you are using a normal power fan, there are some crazy ones that draw close to an amp or more and spin at over 5000 RPM those will hurt the board, but a normal one wont put any undue stress on the board, the fan header's whole job is to power fans, it doesnt hurt it to do so.
Depends .... in cases liek the Antec 1200 / DF-85 where the case manufacturer provides speed control (variable speed knob or 3 speed switch), I'd connect to PSU.
Where 3 pin fan ends are provided and no speed control, I'd connect to MoBo. Enthusiast boards from Asus for example are rated for 2 amps .... most boards however are limited to 1 amp. I'd recommend not exceeding 50% of that to allow some room for inrush current.