lionheart, you are not alone.
I am in the same boat as you... I want to push my career toward open-source. The work is more interesting, the technology is more exciting, and (let's not forget) on the average, the pay is better. There's also a bit more glory in getting a solid open-source solution working. It just feels better. But there are a lot fewer jobs in the open-source realm than there are in the Microsoft world.
Judging by the year at the end of your user name, and correct me if I'm wrong, you are in your late twenties, which is exactly where I am. So we've got quite a bit in common. Let me share with you my plans, as far as the transition to open-source is concerned.
When I started the search for the job that was going to start my career, I went out with the idea that I could convince companies they should look at open-source. I went into interviews preaching the good word about Linux and BSD and all that. That was the exact wrong approach.
After figuring out that I wasn't going to get gainful employment this way, I changed my approach. It sucks realizing that you've got to live with things for a while, but after accepting this as a fact of life, I went back out and got myself a job at a small company doing run-of-the-mill IT work... fixing computers, helping people with software issues... the usual. After a while, I started getting into bigger projects, such as designing and coding our company intranet website, helping to implement a new VoIP telephone system, and deploying a standardized PC platform throughout the company. In other words, I started becoming one of the IT decision-makers, not just a helpdesk support person.
Where am I leading with this? It all comes down to resume. Since there are so few jobs actually WORKING with open-source solutions, those jobs are much more competitive. To make any sort of impression on potential future employers in the open-source arena, my resume has to look pretty decent on that front. What I've been able to do is get my current employer, which is a Microsoft shop, allow me to experiment with open-source solutions. For example, the intranet site that I mentioned uses MySQL as its database backend. So MySQL administration goes on my resume. We're going to be migrating this same site to a LAMP setup, so Linux, Apache, and PHP can be added. See what I'm getting at?
It can be frustrating, because we know how beneficial open-source solutions can be. Stick with it, learn as much as you can on your own, and don't pass up a chance to convince your current employer how valuable open-source can be to their bottom line.