Hi, can i apply for my wife ITIN, she is in H4 and will not be in usa for a while.she was with me in usa between sept 2015 to jan 2016. can i file jointly.

You will be able to file jointly with your spouse for tax year 2015 ….

However you will need either a social security number (if they are eligible) or a taxpayer identifying number to include your new spouse on your return.  Use IRS Form W-7 to apply for a Taxpayer Identifying Number.  A copy is here: http://www.irs.gov/pub/irs-pdf/fw7.pdf .  You need to attach your federal tax return to the application.

The tax return and W-7 are mailed to:

Internal Revenue Service
Austin Service Center
ITIN Operation
P.O. Box 149342
Austin, TX 78714-9342

When the number is issued you will receive a notice in the mail and the federal return will be forwarded for processing automatically. If you will need to file a state return as well and you have not gotten the ITIN by 4/15 then file a state extension and complete the return when you get the number. 

Also:  "You may also apply using the services of an IRS-authorized Acceptance Agent or visit an IRS Taxpayer Assistance Center in lieu of mailing your information to the IRS in Austin. TACs in the United States provide in-person help with ITIN applications on a walk-in or appointment basis. Applicants outside the United States should contact an overseas IRS office to find out if that office accepts Form W-7 applications. The IRS's ITIN Unit in Austin issues all numbers by mail."

Per the answer from bine22 :

Filing jointly might be beneficial, but it definitely not always is.

You have three options to file:

1. Married filing separately (or HoH if you have a qualifying child). You would have to print your return and write NRA in the box for your spouses SSN/ITIN and file on paper.

2. Married filing separately (or HoH if you have a qualifying child) and claiming an exemption for your spouse if they had no US source income. In this case you would need to apply for an ITIN together with your tax return.

3. Married filing jointly. You would need to add a statement that you both choose to treat your spouse as resident alien and apply for an ITIN. However, in this case your spouse would have to report worldwide income as well, but would be able to use the FEIE and/or foreign tax credit.

You need to carefully evaluate your options and choose the best for you and your spouse. They might not want to expose their income to the IRS, even f it's more beneficial. 
If you yourself are eligible to use the Foreign Earned income exclusion and you income is less than the maximum exclusion and you don't have any other or very little taxable income, filing separately is probably the best option.

Have a look at publication 54:  https://www.irs.gov/pub/irs-pdf/p54.pdf

Hello,
I have a question on the above mentioned comment. "You would need to add a statement that you both choose to treat your spouse as resident alien and apply for an ITIN."

What statement is needed? I am filing jointly this year. I have the below forms.
1. filled W7
2. form 1040
3. Schedule B
4. 8889
5. 8965-Health Coverage Exemptions (since she came to US only in Sep)

Is any other statement needed saying that we are choosing to file jointly?

Just add a note saying that you are choosing to file a joint return and  treat your spouse as resident alien and  report total world wide income on this return.   Nothing fancy.

Thanks for the response