The 512MB 250 is a bit more powerful than the 512MB 9800GT, which would in theory make it the better card. Using newegg as a reference though, the 9800 GT is quite a bit cheaper if you choose something like the ASUS one which with rebates comes down to only $70, compared to an MSI 512MB GTS250 I could see being $85 with rebates included. So it really comes down to the matter of how many more points you get for your extra $15.
After a reading a few different searches it appears that people are seeing around 4.5k ppd on a 9800gt depending on WU. A 512 GTS250 seems to come in a bit over the 6k mark. Meaning you get 5 more points to your hard-earned $ with a 512 GTS250. I couldn't find an specific numbers for a 1GB GTS250, but I'd imagine them to be a little more, then they come in at ~$100 with rebates, so it might not be worth it.
I'm no folding pro, so that's purely from looking around, not my experience. Hope it at least helps a little.