Ubuntu – Will the current Gnome desktop be preserved when upgrading to 11.04

Nobody knows for sure, but it seems highly likely. From what Mark Shuttleworth (founder of Ubuntu) said today it sounds like there is a push for polish towards the next LTS release. Based on that it seems highly likely Unity will be kept as the default interface until at least 12.04

In short, probably not.

Forgetting the desktop, there were a handful of applications that I had installed on a Lucid -> Maverick box that were removed by Natty B1 installation because of missing dependencies. These weren't mainstream applications - most of which are maintained and thus version compatible with the Natty libraries, and none of them were critical to what I do so I don't remember which were removed.

Unlike that other operating system, there isn't the overbearing market need to ensure that your copy of Lotus 1-2-3 from 10 years ago still runs on the new shiny.

If you've got hundreds of users, surely one of them won't miss their computer if you "borrow" it as a sacrifice machine. Failing that, carve off some disk, or get another disk (they are stunningly cheap these days) clone off your config and upgrade the copy to see how insufferable the damage is. It may also be useful in your environment to be able to dual boot Maverick/Natty as needed.

Added: You are asking for a guarantee that only empirical testing can afford you. Ubuntu is such a hypercomplex maze of interdependencies that given a huge static survey of your current installation, I'd be hard pressed to give you a definitive answer to what will change or break. If this wasn't so, you could just upgrade the packages you wanted. But you can't do that without entering dependency hell which the modern distros work so hard at avoiding.