Saqqara lies approximately 30 minutes south of Cairo. There is no public transportation from Cairo to Saqqara, nor within Saqqara itself. The best means of transportation to the necropolis and within its vast 7km x 1.5km area is private car, which is exactly what my travel companions and I did. We rented a car and a driver from our hotel for the day to take us to Saqqara first, then to the Giza Pyramids. The trip took about 5-6 hours and cost LE 900 (approx US$160 - as of December 2007). It is possible to combine other sites, such as Dahshur and Memphis on the same trip as well.
I decided not to use public transportation to see the different pyramids outside Cairo (Dahshur is not easy to reach by public transport), but to pay for a car with driver. I asked at the travel agent, which is open a few hours a day at Garden City House Hotel. There was no one to chare the price with so finally I went alone. For the transport to Dahshur, Memphis, Saqqara and the pyramids at Giza I paid 150 pounds. All sights are close to Cairo and with a car they can easily be seen in a day.
You can use public transport to get near to Saqqara. But you will have to change several times and it will take a long time. Then there will be a 1,5 km walk to the ticket office and then much more, to see the pyramids and tombs.
Although it is possible to reach Saqqarah by public tansport [minibus], it is easier to hire a taxi.
I usually reckon about 70 pounds for the round trip and having him wait while you tour the site. As some of the sites are widespread it is useful to have a taxi to move you from one area to the other. It is possible to walk if the weather is cool, but it is not easy walking in sand, so all in all a taxi is the best alternative.
Let's face the sad truth: it's impossible to visit Saqqara without some form of transportation. The necropolis is just too vast, the attractions are very spread out, and even the Step pyramid of Djoser is definitely far from the entrance.
So you'll need a taxi - which you can rent for the day, and visit Giza and Saqqara, and even Memphis if you feel like it. You can stop one yourself in town, but not many taxi drivers speak english, so it might be difficult to negatiate the ride and price, unless you speak arabic. It might cost a bit more if you ask your hotel to organise it, but you should have less hassle. This, of course, only in theory.