You can submit your Income Tax Return on-line by following process - without submitting your Form 16.
1. Go to http://incometaxindiaefiling.gov.in/portal/index.jsp
2. Register and create user (username will need to be your Pan Number)
3. Go to https://incometaxindiaefiling.gov.in/portal/individual_huf.do
4. Download the ITR-1 form
5. Fill the form
6. Cross Check the form for correctness.
7. Generate barcode
8. Next generate .xls(the excel file) and save on your system
9. Then go to https://incometaxindiaefiling.gov.in/portal/login.do and login again
10. Click on submit return.
11. Upload xls file.
12. Click on upload.
Once you have submitted your return, you're done.
The best thing is that you can also check your refund status if any.