Here is a table of states where Intrade disagreed with FiveThirtyEight on one of the first four dates for which I saved FiveThirtyEight data or where they were both wrong on July 24. The numbers are probability of a Democrat winning the state’s electoral votes, with the Intrade forecast first and the FiveThirtyEight forecast second.

On July 24, both sites predicted Florida, Indiana, and North Carolina wrong. FiveThirtyEight got Indiana right on Oct 1 when Intrade was still wrong, but Intrade got North Carolina right on that date (just barely) while FiveThirtyEight rated it a toss-up.
Intrade got Nevada right on July 24 (just barely) while FiveThirtyEight got it wrong (just barely).
For Virginia, Intrade was right in July and August while FiveThirtyEight was undecided and then wrong.
FiveThirtyEight got Colorado wrong on September 14, but Intrade didn’t.
FiveThirtyEight got Ohio wrong on August 22, while Intrade got it right.
Intrade rated Missouri a toss-up on July 24, while FiveThirtyEight got it right.

On September 14, FiveThirtyEight was fooled by McCain’s post convention bounce by a larger margin than Intrade, but by Oct 1 FiveThirtyEight was more confident about correcting those errors.
For states that were not closely contested, there were numerous examples where Intrade prices where closer to 50 than FiveThirtyEight. It’s likely that this represents long-shot bias on Intrade.

In sum, Intrade made slightly better forecasts for the closely contested states through at least mid September, but after that FiveThirtyEight was at least as good and more decisive. Except for Intrade’s Missouri forecast on July 24, the errors seem largely due to underestimating the effects of economic problems – errors which were also widespread in most forecasts for other things affected by the recession.

In the senate races, I didn’t save FiveThirtyEight forecasts from before November 1. It looks like both Intrade and FiveThirtyEight made similar errors on the Alaska and Minnesota races.
[Update on 2009-01-13: contrary to initial reports, they apparently got the Alaska and Minnesota races right, although there's still some doubt about Minnesota.]

On the other hand, Intrade had been fairly consistently (but not confidently) saying since early July that California’s Proposition 8 (banning same-sex marriage) would be defeated. Pollsters as a group did a somewhat better job there by issuing conflicting reports.