Charles Nutter in his blog entry -- Promise and Perils for Alternative Ruby Impls [1] -- makes a fairly detailed analysis of the state of alternative Ruby implementations. He talks not just about JRuby but about all the others as well. The comparison despite all existing biases seems fairly neutral.

A few interesting (according to me) things in that blog post are:

• Ability to run Rails faster (than Matz's Ruby) is an important metric for comparing alternative implementations
• Matz's Ruby needs to improve in terms of performance
• Implementing Ruby on the JVM is a "monumentally hard" task
• Ruby in Ruby is not 100% pure anymore and C code is creeping into it
• IronRuby team does not yet understand the scope of what's necessary to run Rails.
• MacRuby represents a possible better way to run Rails on OS X. 
• XRuby and Ruby.NET are not viable anymore
• HotRuby, MagLev and IronMonkey are the new flavors out there

 Why not read the post and make your own conclusion!