One area of trouble for anyone with a lot of projects is orphans. Those are those projects or tasks that somehow fall off the radar and fall apart not because you are actively ignoring them or prioritizing them as “on hold” but instead because you forget about them. An orphan may be unimportant but it may also be mission critical. Ignore them at your peril.
If you follow GTD, you should not have many orphans because the system requires you to review all your projects on a weekly basis. While I use elements of GTD in my planning, I don’t adopt the system entirely and I don’t review all my projects weekly. Instead, I use the OmniFocus review feature to set custom review times depending on a project’s priority. If I’m working with a client on a big contract, I’ll get a review reminder every week. If I’m just maintaining a corporate book for a client, I’ll only get a review reminder every six months. Although my longer delayed project reviews could cause me a problem, I’m pretty good about starting new projects for anything that requires a more frequent review frequency. Another thing I do while reviewing projects in OmniFocus is assessing the project’s current review frequency and consider whether it needs adjusting.
OmniFocus is the only task app I’m aware of that includes a review mechanism but you could put something similar together yourself in other apps. Just add a task inside projects called something like “Review Status” and set it to repeat at some reasonable frequency.
There also isn’t anything wrong with just taking a few hours every month or two and doing a top-to-bottom audit of your task system. This even works for the paper and pencil crowd. Every time I do one of those audits, I feel better afterward. Moreover, during audits I sometimes do find an orphan lurking in my system and, even better, a few projects I can kill.