Assuming you are not legally separated, you can either file jointly with your spouse or separately.
To file jointly, both spouses must consent and sign tax return.
It is your responsibility to file your tax return each year. If your spouse will not consent to file jointly, then you should file married filing separately status for 2005 and 2006. You will need to obtain whatever paperwork that you need (or copies) so that you can file your own tax returns.
If she will not part with the paperwork, you should try to assemble it the best you can, such as asking employers for duplicate W2, asking banks for duplicate 1099, etc.