The source of your income doesn't affect your right to file joint returns. If one of you gets a W-2 for regular wages and the other gets a 1099 -- which records self-employment and investment income -- you can still file your return together. The only requirements are that you're married and that both of you agree to file a joint return.
Filing a joint return works the same regardless of the source of your income. Add up the total taxable income for you and your spouse from all your 1099s and W-2s. Then add in anything that's not on the forms. Your spouse's self-employment clients don't file a 1099 if they paid him less than $600, for example, but he still has to report the income. Fill out the appropriate tax forms and submit them with a payment for the balance due, if you're unlucky enough to owe tax.
Married couples can choose to file jointly or file separately. Filing separately is not the same as single: Separate married filers above a certain income level pay higher tax rates than singles. Joint filing offers better rates than either, and it qualifies you for several tax credits that separate filers can't use. If you live apart from your spouse and care for a child, you may also qualify for "head of household," which gives you more tax breaks than filing separately.
Filing a joint return if your spouse is self-employed can get more complicated. If your spouse expects to pay more than $1,000 in tax, he has to pay estimated tax during the year -- the self-employed professional's substitute for tax withholding. For each quarterly payment, your spouse figures how much tax he owes, which requires taking into account your income and your tax withholding as well. When you make out your joint return, you subtract his estimated tax -- just as you subtract your withholding -- from your total tax obligation, to see if you owe money or are entitled to a refund.
Sometimes filing separately works out better than a joint return. You can only claim medical expenses greater than 7.5 percent of your adjusted gross income; if the bills are all yours, 7.5 percent of your separate income is a lower benchmark to achieve. If you worry about your spouse making serious tax errors or hiding income from the IRS, filing separately shields you from any liability for your spouse's tax debts: joint filers are equally liable for each others' tax debts.