Planning the trip was time consuming but a lot of fun. I ended up doing the whole thing myself without the help of a travel agent. To start, I'd get Fodor's The Complete African Safari Planner. It will open up your eyes to the innumerable amount of options for your safari. There really are safaris for every budget and taste from camping to luxury safaris to walking safaris.
The first thing to decide is if you want a safari in eastern Africa (Kenya and Tanzania) or southern Africa (South Africa, Namibia, and Botswana). We kind of automatically fell into the southern Africa category. We were using our miles to get to Africa and it was much easier to get to South Africa than the eastern part. Because of this, I can't really speak to the options in Kenya and Tanzania.
Doing a safari in Kruger National Park can be really cost effective. There are small, inexpensive lodges to stay at and you can drive around in your own car. Having never been on safari, we weren't sure about the driving thing. Would we be able to see anything? What if we got lost? We decided we wanted to do a luxury safari in a private reserve near Kruger. I researched all the private reserves in the area and countless numbers of lodges. Most were easily ruled out by looking at prices. There are a large number of lodges that are $2000 per night. Finally I settled on Elephant Plains. Elephant Plains is one of the "cheapest" luxury safari options yet also gets rave reviews. They also have a large area traversing area which consists of their own property and neighboring properties they have agreements with.
There are many other areas to go on safari in South Africa besides the Kruger area. We decided on Kruger since this was our first time and we knew the game viewing there was excellent.
There's also safaris in Botswana and Namibia. We crossed those off our list just because there was a lot of time and expense involved in getting there. Flights from Johannesburg to Windhoek or Maun were pretty expensive and not very frequent and then from there we still had to get to the smaller airports and lodges. We'd like to go back eventually but for our first safari we went more of the path most travelled.
If you have any questions leave me a comment and I'll answer.