There's an interesting statistical comparison between the 1994 Republican victory and the 2006 Democratic victory at the Columbia stats blog. From the post:
The Democrats' victory in the 2006 election has been compared to the Republicans' in 2004. But the Democrats actually did a lot better in terms of the vote. The Democrats received 56% of the average district vote for the two parties in 2006, whereas the Republicans only averaged 51.6% in 1994.
The post also has some comments, and links to papers, discussing the fact that Democrats got a higher percentage of the vote (nationwide) than seats in the House.