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Totally agree about Word etc. It's whatever you feel comfortable with. You could even use Excel quite nicely (for sources especially), I reckon (and just export as CSV). And yes, OneNote. My colleague was an evangelist for it but I couldn't get my head around it.
I get you re cross platform too. I nearly had a meltdown in my early mac years. I just couldn't believe what wasn't available for the mac. I've still got a win laptop but I'm almost exclusively mac these days (the laptop is for Access which doesn't mac).
I do have an Evernote pro account but I discovered that I had to email the notes etc to myself. That was a step too far for me. Whatever I use has to be able to available if I'm offline. But yes, it could totally do the index card thing.
The problem is...too much choice.
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