This is a great reason to not believe everything you read on the Internet. I don't know anything much Java, but I do know a thing or two about .NET and most of the items on that list are plain wrong.
Here are a few of the more defamatory ones (with my comments):
"An Abundance of Experienced practioners. Nobody seems to know how to write .NET programs well and that's giving .NET a bad name"
I know a fair few .NET developers - C#, VB, Delphi and even COBOL. I can assure you they know what they're doing.
"Industrial Strength Collection Classes - The .Net libraries look like they were designed by high-school students, First year CompSci? students at best."
The writer obviously hasn't heard of Anders Hejlsberg who would be in my all time top 10 Software Architects.
"More Languages - The JVM is more "common" than the CLR."
This to me seems to be two seperate points, but I'll take the "More Languages" argument. Here's a list of .NET languages off the top of my head: C++, C#, VB, COBOL, Object Pascal (Delphi), Python, J#
"Sane Coding Conventions - I don't know what's worse Hungarian notation or .NET coding conventions."
Surely sanity is in the eye of the beholder. I like the .NET conventions, plus Intellisense and sensible names in the class library mean I know the the difference between a namespace, class or method name.
"EmbeddedDevices - Java inside small packages."
If you don't count PocketPC's or SmartPhones as Embedded Devices.
"Comprehensive RDMS Driver Support - Can you find a ADO.NET driver for an open source database?"
"Leads In Software Process Best Practices. Most best practices in software development are done in Java shops."
This is clearly wrong. I myself and most of the .NET developers I know use some or all of Patterns, n-tier design, Unit Testing. I don't think SoftDev best practice is limited to Java.
"Affordable Industrial Grade IDEs"
SharpDevelop, WebMatrix, Visual Studio Express are all free. Borland Developer Studio professional is about $300US.
I could go on but I won't. There is a challenge out by the original author to make an anti-list of why .NET is better than Java. I would love to but don't know enough about Java.
Besides, I would rather spend my time programming in .NET - its much more rewarding...