A Slashdot article (http://developers.slashdot.org/story/09/06/10/2142256/Yahoo-Releases-Open-Source-Hadoop-Distribution) points to the fact that Yahoo! will release its own version of the Apache web server. Yahoo! has used the Hadoop (http://hadoop.apache.org/core/) variety of Apache for years in its search engine and now some of those special modifications can be used under an open source license. What makes Hadoop unique is its ability to process vast amounts of information while in a cluster. The official Yahoo! announcement can be found at http://developer.yahoo.net/blogs/hadoop/2009/06/yahoo_distribution_of_hadoop.html.

The facts as given are not directly related to Yahoo! Messenger but this may give an indication as to what server software Yahoo! is using for Messenger. To my knowledge Yahoo! has never stated what is running Messenger on the server side of things but I have seen an Apache signature many times.

http://developer.yahoo.com/hadoop/
http://ostatic.com/blog/at-hadoop-summit-yahoo-announces-its-tested-distribution