Intel processors include an architectural feature called "Hyperthreading" which is an optimization that allows a single CPU to have some of the performance advantages of multiple CPUs. More information about Hyperthreading can be found on Intel's Web site.
Blackbaud products have been tested on Intel processors with the Hyperthreading feature and no known problems or compatibility issues have been found. Based on Intel's documentation this is to be expected since the Hyperthreading feature is a low level architectural implementation detail that is abstracted from application software, much like other CPU features such as Level 2 Cache size, processor speed (Ghz), or bus speed.
The Hyperthreading feature allows the Operating System to treat a single CPU as 2 distinct processors. Usually only certain software applications will take advantage of multiple processors, either real or virtual, as is the case with a Hyperthreaded processor. Such programs are said to support multiple "threads" of execution, in which individual threads can operate in parallel on a real or virtual CPU. Such programs are said to be "multi-threaded".
Blackbaud client-side components (The Raiser's Edge 7, The Financial Edge, and The Education Edge "shell" applications) are single threaded and therefore should not gain any advantage from the existence of multiple processors, nor should they suffer any disadvantage.
However, server side components such as the Microsoft SQL Server database engine, the Oracle database engine, and Blackbaud Web products running on Windows Server Internet Information Services (RE:Anywhere, NetClassroom, Faculty Access for the Web, NetCommunity, etc.) are multi-threaded and thus have the potential to take advantage of the existence of multiple real or virtual processors. The detail of how many and what kind of processors are handled by the Operating System (Windows) and is usually abstracted from applications. Refer to Microsoft's Microsoft Windows-Based Servers and Intel Hyper-Threading Technology for more information on Windows support for multiple processors, specifically hyperthreading.
Your machine's BIOS may also have a feature to disable hyperthreading. However, there are no known issues with Blackbaud client or server side software that would require disabling hyperthreading. Therefore, it is recommended that you leave Hyperthreading enabled unless you identify a specific compatibility issue causing a problem.