I'm in US since Aug 2006 with F1 visa (and F2 my spouse).
Nothing changed in 2007, and I didn't leave US at all.
Then in June 2008, my visa status changed to H1B (and H4 spouse).
I am also receiving tuition waiver as employment benefits (I got the 1098T form).
Spouse does not have ITIN and never filed any returns in US.
I have always filed 1040NR-EZ (for 2006 and 2007) but didn't claim spouse these years (on F2)

My question is whether I have substantial presence in US after 3 years or not, and which form should I file. How about spouse (with no ITIN)? Thank you.

One more thing: is it a problem I didn't request for an ITIN by now? Should F2 always have an ITIN even if spouse have never had any income of any sort?

File joint resident return as married filing jointly. Attach W7 (ITIN application) for your spouse.

Assuming that you have filed and received your wife's ITIN, you may want to amend your 2006 and 2007 return to claim your wife as a dependent.

This is allowed if you are a citizen of India, Mexico, Canada or South Korea.

Email me at [email protected] if you need professional help amending your returns.

Filing jointly for the whole year allows you to avoid the complicated dual status return.

Assuming that you have filed and and received your wife's ITIN, you may want to amend your 2006 and 2007 return to claim your wife as a dependent. This is allowed if you are a citizen of India, Mexico, Canada or South Korea.

What if I'm not a citizen of those countries? No amend necessary, or no dependent claim possible?

Right. No amending necessary.

My status just changed from academic professional to civil service employee, due to "bad economy" reasons.. I guess.. my question is how could this affect my H1B visa and/or my current tax status ?

For 2008, you can file jointly with your wife and CHOOSE to be treated as a resident alien, filing a normal tax return (Form 1040). Not that to make this choice, you MUST file jointly.

For every successive year, you will also file as a resident alien, either jointly with your wife or filing married filing separately.