I have to move a cold air return in the basement and want to know which option would work best for me and if there is anything i need to be aware of.

The current cold air return is taken directly off the trunk in the basement ceiling about 3 feet from the furnace. A 7", 90 degree duct take-off is attached from the trunk to sheet metal between the joists of the furnace room wall, where a vent is located near the floor on the other side of the wall (into the finished part of the basement). I need to move this vent to accomodate a wall-bar I am building.

What option would be best?

1) Take out the 90 degree take-off, patch up the hole in the trunk, and move the vent to be directly in the ceiling off the trunk on the other side of the wall? (I was told its better to be vented near the floor to get the cooler air)

or

2) Move the sheet metal backing on the wall to another set of studs located in the wall about 6 feet away, which would mean I would also need to add about 6 feet of 7" ducting to attach it to the new area, and add another 90 degree turn (meaning there are now 2 90 degree turns in the ducting from the the trunk). Would this be ok as this is my preferred option ... will this somehow upset the airflow with the additional length of ducting and the added 90 degree turns?

Your second option would be fine.

If your installing a base cabinet you can always put the return under the toe kick area. Just get a 3-1/4 by 14" duct and tye it into the panning of the existing wall and carry it through under and into the room at the floor level. Flare the end out and screw a grill onto it.
Ideally the duct should be near the floor in the basement to pull the cold air back. But its not mandatory do to so.