[Lizard]

OmniFocus is good if you want to keep all your tasks loose and unscheduled. OmniPlan may be better since it sounds like you want to plan everything out. It might be overkill (since it allows for more than just one person working on tasks) and has some limitations. You might also look at some timesheet or other scheduling applications. Anyone out there got suggestions of apps more custom-tailored to this scenario?

Here's some thoughts about using OmniPlan in the way you describe:
1) OmniPlan has no simple way to show a task being worked on in multiple time blobs, interrupted by other activities. Option one: accept that the task's duration will not match how many hours you spent working on it, but rather how many working hours passed between start and finish. Option two: When a task is worked on in pieces, create sub-tasks under it, so that each one can have its own start and end time, even if they don't represent logical blocks of work. So "Build Framistan" might have three sub-tasks, "Build F, interrupted by dinner", "Build F some more" and "". The first one runs 4-6 pm. The second might be 8-10 am, and the third 1-2 pm. The total duration for "Build Framistan" will then correctly be 5 hours. (10 am-1pm went to "spent 3 hours fixing bug 1090", which would be recorded as a separate task not under "Build Framistan".)

2) When you've got your initial schedule, you can click the "Set Baseline" toolbar button to sort of archive those baseline start and end dates for each task. Then, when you really start to work on a given task, you should adjust its actual start date. If you also lock the task's start date at this time (command-click the left end of the task in the gantt chart), this task will not be moved by leveling. That way unstarted tasks are still free to re-level as needed (new dependencies or deadlines, etc.) but stuff you've already started on won't move.

3) If you're only tracking your own work, you can use milestones to represent external events that affect your scheduling. For example, create a milestone that represents when your colleague says he will hand off data to you. Then any of your work that depends on this data can have a dependency on that milestone. If your colleague says he'll be late, you can just move the milestone, and OmniPlan will help you see what other tasks need to be delayed, and you can adjust them manually, or run OmniPlan's leveling algorithm again.

4) When you need to compare your current schedule to the original plan, you can switch from "Actual" to "Split Schedule" in the toolbar. Tasks where the top and bottom half line up are on-schedule. Anything where they're mis-aligned have been re-scheduled for some reason. And if a task has no bottom half, that means it was added after you created your baseline schedule.