My employer is not showing any of the medical I pay on my w2. So the amount of wages is off by almost $3000. Shouldn't this be shown somewhere on the w2 since it is money I worked for and paid for my benefits.

The amount you pay in deductions other than tax withholding, will not be listed on your W2. Taxable income may be lower than gross income, if there are pretax deductions (like health insurance premiums).

Your federal wages will usually be lower than your gross wages because certain deductions are made with "pre-tax" money, essentially avoiding tax on the portion of your wages used for these purposes. Such deductions include medical/dental premiums, 401(k) plan contributions, and any flexible spending account contributions you make (for medical or dependent care purposes). On the other hand there are certain benfits that that are taxed even though you never see the cash in your paycheck. For example if your employer provides life insurance for you in excess of $50K, the government assumes a cost for the premium for that excess amount and you pay income tax and FICA on this excess benefit.