Though my answer is posted after a while, I am sure it will help many viewers.
You have mentioned that you have gone beyond excel spreadsheet & index card, which are inherently not collaborative. However the good news is - cloud based software are at your disposal, really.
You can take trial, evaluate the software for free of cost
Only if you are convinced of software, you can decide to purchase subscription (pricing is transparent in most cases)
These subscriptions are really cost-effective compared to on-premise or enterprise application however you still get equivalent functionality or even more collaborative
The important criterion for you is scalability in terms of number of projects & could be number of users also. So you can evaluate cloud based software with reference to these parameters.
Answer
Though my answer is posted after a while, I am sure it will help many viewers.
You have mentioned that you have gone beyond excel spreadsheet & index card, which are inherently not collaborative. However the good news is - cloud based software are at your disposal, really.