I can give you my personal account. I started riding Gas Gas in 1999 on an EC 200. Since then I have had a 1999 XC 250 Six Days, a 2001 ECO 300, and now a 2008 EC 250.
It's interesting how the 300 and 250 compare. They are both fine machines. Frankly if you want one, and it's not available, the other is just as good. The 300 has slightly more chug right off of idle, and I'd say the 250 revs more freely on top. Aside from that, they seem to make about the same amount of power overall. I will say that it seems as though the 250 is a bit less tiring to ride over a long day. Really, they are so close it's too close to call. if there's a price difference between two sitting side by side, I'd take the less expensive one.
On a side note, the 250 seems to me a little easier to get the jetting sorted out on, but that could be circumstantial to my experience only.
Both bikes benefit from the RB-Designs head mod, and at only $75 it's the best money you can spend on a bike, especially considering the added fuel economy it yields. Outside of fresh tires, and any guards/protective equipment you might want, this is the best performance mod for the bike. I almost forgot about the LTR power valve cover. I have had one on all of my gassers except the 200, and that extra volume helps the lower rpm snap as well.
Bottom line, the 250 and 300 are both great, and the only reason I'd purposely choose one over the other is to pick a class to race in. For instance if you wanted to ride E-3 instead of E-2. It really is that close. At least for me.