SharePoint and XenApp Integration: Why

It depends on what you're planning to achieve.

If you're going to have a small farm with small quantity of users, then this is something you don't have to take in consideration. However, when you're deploying a really large farm you should pay attetion to software boundaries.

As you can see in this Technet Article Plan for Software Boundaries, SharePoint degrades performance exponentially when certain things are not taken into account.

I would suggest you pay attetion to these performance issues, rather than site collections. Site Collections have their pro's and con's, however when you're working with large farms (100GB+), Microsoft suggests to use a single site collection and quotas for content databases. Hope this helps.

-Máximo

You're right... out of the box, having SharePoint groups with thousands (or even hundreds) of individual users will be an administration nightmare.

Unfortunately SharePoint doesn't sync AD users with with AD (profiles, yes. users, no.), so once you have manually add a user to a SharePoint group or manually grant permissions to an individual user, they will remain in Sharepoint for all time (until you manually remove them), even if you remove that user from AD.

If you assign permissions to SharePoint groups holding AD groups, you gain the benefit that once a user is removed from AD, they no longer have permissions on SharePoint. It is so much easier to manage group membership in a single location (with good tools) than it is to manage group membership twice.

Long story short, I would suggest trying to figure out the problem you are hitting with audiencing before I would suggest putting a thousand users in SharePoint groups. If you absolutely must do so, don't do it with out of the box tools... invest in Quests's Site Administrator for SharePoint (http://www.quest.com/site-administrator-for-sharepoint/)