This will eventually be a fairly full-fledged guide to the process of developing a base configuration and then installing applications on Terminal Services.
Terminal Services is usually very good at handling installs itself; unfortunately, certain applications need assistance.
Some notes used as a guide for staff at UC-Davis Crocker Nuclear Laboratory; focused on Citrix on NT4TSE, but useful for Win2K and .NET as well.
A start on notes for adjusting the UI and user config before application installs even begin.
For various reasons, there are some applications you simply almost never attempt to install for general Terminal Services access.
Some are illegal to use on TS (fortunately not very many - and the real cause of the prohibition is usually that the OEM has become "aware" of TS enough to be concerned about licensing, but not aware enough that it gives them extra licensing control) . Some will install, but will not run over a remote session or will be notoriously poor in how they run (e.g., depend on high-color and use it extensively). Certain others just don't work well on NT platforms, notably some notorious early 1990's database apps which continually poll the keyboard.
Notes on some best practices and general notes or lists of applications which are known to have successfully been installed on some version of TS with or without Citrix.
Despite some possible issues with Adobe Acrobat Reader 5.05 on TS, Adobe is generally a TS-aware software OEM. This page has some notes on finding out more about specific Adobe products.