Our accountant suggested Property Manager Pro. Works good for us. depending on your own circumstances you can treat yourself and trusts as properties for working out your profit/losses. Only about 100 bucks from Officeworks and definately saved me more than a few hours.
Might be worthwhile getting a demo / trial version of a few different programs, and then order the one that *you* find most comfortable and easy to use.
Your accountant should be able to make sense of just about any of them (assuming you've done things properly!) so don't stress too much about that side of things. I know full well that record-keeping is a pain in the proverbial (you know that saying about mechanics with poorly-kept engines...? ) so make sure that you're happy with the software before worrying about whether your accountant is.
Good on you for making an effort, though. Should be helpful for your own decision-making processes, too, if you have up-to-date information with which to do so.
I have used the Quicken product Personal Plus since 2000 (about $200) for managing all of my finances. I have my IP's set up as there own assets and cost categories so that income and expenses are allocated to each one. At tax time I print off a tax report and take it to my accountant - so easy .
I have budgets, forecasts and can do easy cash flow analysis. You can set up and track all of your loans (including LOC's). When I want to buy a new IP I am able to print out cashflows and net worth reports for the bank. They love this level of detail .
Takes a bit to set up properly but takes me less than 20 minutes a week to enter purchases and update bits and pieces.
Obviously Quicken can't do an analysis on what property you should buy, so I rely on PIA for this .