One major inconvenience is that most Cydia apps are not iOS 4 compatible yet. To avoid the headache and maybe even a system restore you can check out this Google Docs lists, which is updated in real time by users. You can contribute as well…
https://spreadsheets.google.com/lv?key=tz1lkTAAwtDi_7HJxef0Vgg&f=true&gid=1