Are there any software packages, that allow to selectively limit filesystem access for each application? Do they have significant impact on system performance?
I haven't used it but Sandboxie may be what you are looking for. Sandboxie runs your programs in an isolated space which prevents them from making permanent changes to other programs and data in your computer.
Sandboxie handles writes by default and it looks there are options for controlling reads. From the FAQ:
It should be noted, however, that Sandboxie does not typically stop sandboxed programs from reading your sensitive data. However, by careful configuration of the ClosedFilePath and ClosedKeyPath settings, you can achieve this goal as well.
Using Sandboxie in combination with a good firewall may give you the isolation you want.