From a career perspective, there will be Microsoft (C#/SQL Server) jobs and there will be Linux jobs, and even some OSX jobs available to you if you market yourself well. (Not to mention of lot of iOS jobs as every company want's an iPhone app these days)
As far as I'm concerned, it won't affect your enjoyment of the job nearly as much as coworkers, commute time, and other company perks; and based on the nature of your question I'm assuming your coming in as a Junior where you would be expected to need to learn the environment when you start anyway. Maintain a passing familiarity with several technologies so you don't sound completely clueless in the interview and can put some nice keywords on your resume, then become an expert in whatever is relevant when you land the job.
As a disclaimer, I work primarily with ColdFusion, C#, Sql Server on Windows Server machines. At home / for hobby projects I use Arch Linux, C++, and php.