Suppose a hacker wanted to write his own programs/system/firewall or build his own commlink at character creation. Since one of the main factors of this is time, considering it takes months to write a single program, how long would you let the characters do this for prior to actual game play? 1 year?

I guess similar questions could be asked about writing your own spell formulas, and building your own vehicles, at least once Arsenal comes out.

I believe the whole point of the BP system to buy gear is to simulate the aquisition of hardware, skills, gear and whatnot before you actually play the character. You can perchase a custom 5/5/5/5 commlink at chargen by using the charts in the Matrix section of the book.

That works for commlinks, but what if someone wanted to start the game with a custom spell? Would you let them just spend the BP on it like any other spell?

Most likely, depending on the spell and the character's background. At this point, you are basicly asking what people would do if they were the GM and not a 'by the rules' yes or no answer.

My rule is 1 month. They can use this for design, breaking copy protection, B/R, pretty much anything their character can do in a month. Beyond that and it's just part of their background and paid for with BP.

1-month-rule aside, yes, I'd let someone start with custom spells, provided they had reasonable Arcana, and I would charge the normal BP cost just like any other spell.