I don't know how much reformatting helps, and I've had freezing problems regardless of what source I got the ROMs from. I stumbled upon another solution here, and I did it at the same time as a reformat of the micro SD.
That said, I can't tell you which one helped the most, but I've gotten only 2 freezes since doing this (and before doing it some games would freeze every time I played and now they don't). Get a jeweler's screwdriver (those really small ones) and take the one screw on the R4 out. Peel the cart apart, being careful not to break off the small plastic pins. I broke two of them, and the thing still fits together fine so it's not a big deal, but just try to be careful. Now, take a small piece of cardstock-type paper, about as wide as the R4. Put it in the case at the bottom of the side where the label is, then put the chip back in and put it back together.
I hope that's a good enough description, but if you have any questions ask away. The concept is that the R4's contacts are kind of loose, and the card slot on the DS is spring loaded. Every once and a while, the contacts, which are a bit loose inside the case (not really enough for you or I to notice, but enough for it to lose contact apparently), don't make full contact and the game just freezes. So what you're doing with the cardstock is making it so that the contacts are more firmly held in their proper place.
Like I said, it worked pretty well for me, I've only experienced two freezes since then.
