I found a series of blogs on how to identify Performance bottlenecks in BizTalk Environments.
Also look at this article on finding and eliminating bottlenecks

Here’s an short overview of all the steps, including a link to the more detailed explanation:

Step 1: Monitoring BizTalk Host Instances via Windows Performance Counters

 The first place to measure the BizTalk performance can be done using Performance Counters. These counters let you monitor all components like the message box, orchestrations, adapters, etc .

Step 2: Analyzing BizTalk Adapters

A deeper look at the adapter performances, again using some performance counters.

Step 3: Analyze Pipelines

It is important to understand the impact of Pipeplines that are used. Because each of the pipelines have a significant impact on the overall BizTalk performance as they perform actions on every single message that gets through BizTalk
One way to analyze what is really going on in pipelines is using an Application Performance Management Solution with Transactional Tracing capabilities, like dynaTrace for example.

Step 4: Analyzing Orchestration

Orchestration can get quite complex sometimes, but how to analyze the performance of these orchestrations?

The actual logic behind the Orchestration Definition is compiled into an assembly, loaded into BizTalk, and gets executed when messages are processed by that Orchestration Definition. A more detailed overview of the execution of such an orchestration can be generated with PurePath for example.

Another way to analyze the orchestration performance can again be done using performance counters.  BizTalk provides a set of counters for the Orchestration Engine as well as for the MessageBox.

Step 5: Analyzing external service calls (SendPorts)

Often BizTalk Orchestration makes a call to an external web service. PurePath can also give you an idea of the time consumed for this external web service call.


As a final note I would like to point out to use the MessageBox Viewer Tool. The tool gives an overview of what might be wrong in your installation.
This tool runs a set of tests and queries against the MessageBox database an creates a nice report. The result can be viewed using the tool or it can generate an HTML report.