Couple ways to achieve this

1. You can disable the auto email population feature. By default, alerts  are restricted to the email address stored in the user  profile and subscribe all your users  using a email alias or distribution list.

a. For sharepoint  Portal Server go to Site Settings, Manage alert settings, and uncheck the box “Always use user profile field ”. Then go to the content you want to setup alerts and subscribe an email alias or distribution list

b. For Windows Sharepoint Services, login with a user without email address, select the content to be alerted, enter the email address of the alias or distribution list


2. Programmatically, you need to build either a web part or some code that will use the object model to subscribe users

to my knowledge this can be done only through code, using Object Model

SPWeb web = SPControl.GetContextWeb(Context);

SPUserCollection userCol = web.Users;

foreach(SPUser user  in userCol)
{
user.Alerts.Add(<list/list item>, <action>, <frequency);
}

this code will work only from a web part. if you try to do it from a .net web
application you will get a Code Access Security error. Also you must remember
that the user must have atleast reader privilages on the site in which the alert
needs to be set.

We are also very interested in this feature. I have tested your suggestion (1 (a)), and it looks to me like what you are doing is replacing your own e-mail address with another one (a distribution list, for example). That prevents you from subscribing to anything else on that site with your original e-mail address (you can only have one e-mail address stored in that site for alerts), and forces you to maintain many different DLs for each occasion.
Is my understanding of what you suggested correct, or is there something else we could do? Just wanted to make sure I was following the instructions correctly.
Thanks for your help,

Why was the ability to subscribe other users  taken away from the
administrator in this version in the first place? It was a VERY
useful tool in version 1 that I'm sorry to see go away. Is there
anything we can do to ask that it be reinstated, perhaps in an
upcoming release or fix? The solutions mentioned here may work, which
is fine, but they are fairly cumbersome to implement, and not all SP
admins may have access to the parts of the system that need to be
changed.

Nothing beats the simplicity of the original ability to subscribe
your users to those features you absolutely need them to see. You can
NOT assume that all of them will subscribe, even if you ask them
nicely :)

It wasn’t taken away; it is there by disabled by default for Sharepoint Portal Server. As far as WSS, it will let you subscribe other users  as long as the login user  doesn’t have an email address in the User Information section.