When I open my BlackBerry Desktop Manager, It says that there are no applications. Do games and other applications download as either .alx or .ali files?

Did you install OS 4.0 on the desktop with the Desktop Manager? Most apps do download with the install extension that you can select when using the browse button. Blackberry desktop mgr works a little differently then palm, with blackberry you have to have the copy of the application residing on the PC to view it as installable applications.
Hope that help!
Dewm

I'm having this same issue. When my 7100t is connected to my desktop, it shows as connected and can sync with outlook, the problem is that when I go to the application loader, it says that there is no software installed on my BB. This is a new problem, as I have loaded software in the past with no problems, and nothing has changed with either my phone or my computer. Can someone help me out with this?

Check if you have the OS installed on your BB Desktop manager. To do this, go in Help, About Desktop Manager in the Handeld Software tab.
If you OS is not list, download it from Blackberry .com