This sounds like an enterprise environment situation to me, so if that assumption is correct, Ubuntu is not the way to go. That distro is more suited to home environments.
Since you're already running VMware, I'll go ahead and assume you're licensed for it... and seeing as how ESX has entered into an agreement with Novell such that you're now instantly licensed to run as much SLES as you have active licenses for VMware, that seems like a no-brainer. SLES is also the distro of choice for business users who are new to Linux, because it comes with some unique automated tool sets that reduce the learning curve. So that's a direction I strongly recommend.
MS-SQL to MySQL should be a fairly lateral move as far as the individual databases are concerned, because ultimately, SQL is SQL. Honestly, I think you'll appreciate the difference. I'm working on an app using an MS-SQL database right now, and I hate it.
VB.net and PHP are whole different animals, so good luck there. That'll probably pose the biggest challenge of the whole project.