This is a great topic. I track pretty specific types of investments, so my programs are pretty focused on the type of property. For my mobile home parks, I use a program called Park Side Kick. It tracks the day to day happenings in the park, and also does the more complex billing that quick-books does not do. Like water bills, sewer bills, electric bills etc. Because these are ever changing due to consumption, they can be tricky to figure out. It also does all of my tenant billing, with mail or email. I still enter the big numbers into quick books, as quick books is great at tracking the income and expenses of your business.
I also use Notesmith to track payable notes to me. If your tracking interest, a program that really understands how interest is tracked is essential. I use this for notes that are payable to me, and when I purchase properties on owner financing, I track my payments to the seller as well. It produces 1098's, 1099's and will electronicly connect with the IRS to transmit your data.
I see posts on quick books set up... there are many 'guru' types that sell accounting courses and many of those will give you the category's pre loaded on a CD. you will need quick books to open the template, but all of the accounts are there. I use the program from John Hyre, The real estate investors kiss guide to bookkeeping. John is a CAP, an Attorney and practices real estate investing, as well as a accounting practice and practices law. I have met him a couple of times, actually had breakfast with him before a seminar he gave in Denver. He is very sharp and the real deal. His stuff is very easy to follow. His web site is www.realestatetaxlaw.com
I have no dog in the hunt to endorse any of the programs I have mentioned here, if there was a better program I would switch in a New York second.