I saw a demonstration of this tool at the workshop on network analysis I announced last week. Genes2Networks draws from a large background network consisting of several experimentally verified mammalian protein interaction databases. It will take a list of genes you provide as seed genes and identify all interacting genes that fall on paths through the background network between them. It then calculates a z-score for each intermediate node based on the number of links to the seed nodes and the number of total links it has in the background network, and color-codes the significant links.
It's free, and it took about 30 seconds to paste in and analyze a list of a few dozen genes I submitted. It looks like a great way to identify potential interaction partners for some genes you've already found. You can also export the networks you find to a text file that can be loaded with other software developed by this lab for more extensive statistical network analysis and visualization.
Publication in BMC Bioinformatics
Avi Ma'ayan's Lab Website
UPDATE 2009-04-27: I have slides from three one-hour lectures that Avi gave on network analysis following his seminar. Email me if you want them.