Kim,
We were on Gibraltar for right at 3 hours and here is what we did:
Cable car to top (and then cable car down), then St. Michael's Cave (disclaimer: we could have used an extra 30 minutes there), then a drive out to the point, and then drove to the entrance of the Siege Tunnels and then toured both sides of the Siege Tunnels.
We had a FABULOUS guide, who met us at the border (we walked across the border), then jumped in his van.
Unfortunately I don't remember the name of the guide (would have to dig thru yet-to-be-organized tourist info to find it); but you can email Emily with South Ole Spain Tours and ask if she can arrange the same guide she arranged for Margaret in Nashville last year. He really was fabulous. I think he is the retired police chief (or some other high ranking position). He told us about the history of Gibraltar and about current life in Gibraltar as we toured. We had a limited time there (due to our own self-imposed timetable), and he made sure we saw all of the our must-sees while there.
Ideally, if you are visiting the Siege Tunnels (which my husband had on his must list, and I really did find them fascinating, too), you need a minimum of 4 hours in order to not rush too much. You can check them out on YouTube. And, we spent no time on the main street of Gibraltar shopping/dining, etc. We just saw the historic sites and then were off to Old Town Marbella.
Emily with South Ole Spain Tours is originally from North Carolina. She fell in love with Spain and now lives there. Check her company out on Trip Advisor. She can do as much or as little as you might like for your trip. We arranged a driver for an entire day (a long day) and then also the Gibraltar private guide. She was very reasonably priced, and she checked in with us to reconfirm all arrangements then to insure we were satisfied (we were totally satisfied.....totally delighted!).
http://www.tripadvisor.com/Attraction_Review-g187437-d2302101-Reviews-South_Ole_Spain_Tours_Day_Tours-Estepona_Costa_del_Sol_Province_of_Malaga_Andaluc.html#REVIEWS
She also offers group day tours for various locations in Spain and Morocco, and she will make turn-key plans for entire vacations, if desired.
Have fun!