The rules for acquisition of citizenship and derivative naturalization are quite complex. A full analysis of all pertinent facts, including dates of birth and periods of residence in the US, is required before making a determination as to eligibility is possible.
If you have an H-1B VISA in your valid passport, and are maintaining valid status, you need not obtain advance parole in order to travel and will not be deemed to abandon the adjustment application. You still must consult with a reputable immigration attorney to make sure you met these criteria.
Depending on when your friend reentered the US after the previous deportation, and the reason he was deported in the first place, he faces serious bars to adjustment of status under current law. It is unlikely that the immigration reform, if passed, will sweep away these problems for him. He should consult with a qualified and experienced immigration attorney as soon as possible to discuss hos options.
If your wife initially entered the U.S. with no visa, then the U visa is an enormous benefit to her. Aside from legal status and work authorization, the grant of U status may be considered a lawful admission, which could make her eligible for additional benefits.
You must file the petition in the US, unless you are residing yourself in India. The F-2A category (Green card petitioner) is backlogged only to September 2013 for India, so I would recommend filing it as a green card holder no. for the quickest result.
If you have been counted against the cap within the past 6 years, then you should not be cap-subject on a new petition. You face several challenges, however, given the history described in your inquiry. Consult with an experienced immigration attorney.