Two things to know about VMware Converter

VMware Converter is a tool to convert physical machines (either online or via an existing backup image) to VMware virtual machines. It is available as a free stand-alone version and in a vCenter-integrated version.
Like others we are using it a lot for virtualizing existing physical servers, just because it's free and/or comes pre-installed with vCenter. It also does a pretty good job and is well supported by VMware, but ...
you should be aware of two issues when using Converter more than occasionally.

1. Windows 2000 support
With the latest versions (Stand-alone converter 4.3 and vCenter 4.1-integrated) VMware dropped support for converting Windows 2000 machines (see the notes about supported guest OSs in the Release Notes). The really bad about this is that it does not just tell you this when you try to convert a Windows 2000 machine, but throws an error message about not being able to install the Converter agent on the target computer. It looks like it tries to install the Windows XP version of the agent which fails.
At first it looks like this is not a big problem, because older versions of the converter still support Windows 2000. If you run vSphere 4.1 you can use the stand-alone Converter 4.0.1 to convert Windows 2000 machines by connecting to the vCenter 4.1 server or directly to an ESX(i) 4.1 host. We have done this a lot and it always worked. However, if you carefully look at the Release Notes of Converter 4.0.1 you will notice that it only supports vSphere 4.0 as virtualization platform, but not vSphere 4.1.
We asked VMware support how we - as a vSphere 4.1 customer - are supposed to convert a Windows 2000 machine using Converter in a way that is fully supported by VMware. Here are the instructions (it's only one possible way, but you will get the idea):
a) Install an ESX(i) 4.0 host and add it to an existing vCenter 4.1 instance
b) Use the Stand-alone Converter 4.0.1 to connect to this ESX(i) 4.0 host and convert the Windows 2000 machine
c) Migrate the virtualized Windows 2000 machine to an ESX(i) 4.1 host (either cold or by VMotion)
That's a bit cumbersome, isn't it? Anyway, as stated above you can also use the stand-alone converter 4.0.1 to connect directly to vSphere 4.1. It is not officially supported, but seems to work quite well.

2. Disk alignment
If you care about storage performance then you want your VMFS volumes and your guest OS partitions to be aligned. There are a lot of good explanations about what disk alignment is and why it is important. My personal favorite is on Duncan Epping's blog.
Now, the big issue is that VMware Converter does not align the guest OS partitions in the target virtual machine. Although VMware is also pointing out the importance of disk alignment since a long time (see e.g. this ESX3 white paper) they have still - as of version 4.3 - not yet built this capability into their own Converter product.
So, if you are serious about disk performance and are planning for a large virtualization project you may want to consider alternatives to VMware Converter. There are other commercial products available that do proper disk alignment. One example is Quest vConverter.

Update (2011-09-01): Good news. Today VMware released Converter 5.0 which is now able to do disk alignments!