Well, that's all you had to say in the first place. Losing access to programs is not good so some forethought and a little extra work are called for.
There're a few ways to reduce entries by combining programs into a parent folder. This creates an additional menu in All Programs where the programs can be selected. This is done by editing the "C:\Documents and Settings\All Users\Start Menu\Programs" and\or the "C:\Documents and Settings\[your login name]\Start Menu\Programs" folders. I recommend editing the \All Users folder as that will have the most entries. Your problem is that there are too many program folders listed in these directories for your OS to list all of them under the All Programs menu.
Open C:\Documents and Settings\All Users\Start Menu\Programs via Explorer, make new parent folders, then drag-n-drop/cut-n-paste groups of associated programs into their new parent folders. Common examples are Business Programs, Games and Multimedia. Corresponding programs are placed inside of the parent folders of this directory and are displayed accordingly in the All Programs menu. When the parent folder is selected in All Programs menu the associated programs will show up on a new menu. This reduces the program folders of the directory to a manageable level.
There are shortcuts listed in the C:\Documents and Settings\All Users\Start Menu\Programs directory (like MS Office apps) which should only be deleted if their program has a folder in C:\Documents and Settings\All Users\Start Menu\Programs with the shortcuts in them. You can rearrainge the icons in the folder or drag and drop them in the Start Menu to suit your preference as the new folders will default to the bottom. Reviewing and confirming each selection before making changes is recommended.
Lastly, when you install certain new programs you'll have to change the install location to one you've created as most programs default their install to C:\Program Files -hence your problem. In that case you simply add the parent folder to the install location such as \Business Programs so the install location appears as C:\Documents and Settings\All Users\Start Menu\Programs\Business Programs or C:\Documents and Settings\[your login name]\Start Menu\Programs\Business Programs.
Not having access to programs or deleting them is not good. This will solve your problem. Plan your consolidation and take your time. Usually Business Programs or Games is all that's needed as these types have the most entries. Good luck.