I saw it first as symbolic, second as practical. (I think we have had a thread like this before, but for the life of me I wouldn't be able to find it or I'd link to it.)
Symbolic: In a way, he's done with his Zen "sit and do nothing" philosophy. Something has clearly changed in him (or so it seems to me). He was willing to sit back and wait... until his kid's life was on the line, and now he's headed out to kick some ass. Not completely, of course-- not in the same way Sam's headed out to kick some ass-- but it's a definite change. Q sees it and she knows immediately what he's going to do. After all, at some point he changed from what he originally wore in-Grid (as seen in the flashbacks). At the time he goes into exile, he hasn't switched yet.
White's generally considered (in our culture) a color of purity, innocence, and peace. Black generally symbolizes darkness, badassery. It may even "get him into the mood" or help change his mindset (I know for me, if I'm in a crappy mood, or about to head into a situation where I need to be tough, my look tends to shift more goth-- it's psychological.) Or, alternately: white in Asian cultures is symbolic of mourning. If Flynn's into Zen Buddhism, he no doubt knows this. So it's entirely possible he wears white to begin with as a symbol that he's in mourning for everything he has lost/everything that has gone bad. His change to black may also mean he is no longer in mourning, as he's about to go out and do something about it for once in a very long time.
Also, almost everyone in the Grid wears black. Flynn has set himself apart, and he wears white. The change back to black may also symbolize that he's heading back into the general populace of the Grid.
Practical: Easier to get around in the shadows.
In this fic: http://www.tron-sector.com/forums/default.aspx?a=top&id=439658
I define it in part as: Black for stealth. Black to signal a change. Black for a fight.
Which pretty much sums up what I said above.