As we all know windowing function or any kind of EQ'ing could destroy transients, introduce ringing artifacts etc...I wounder is there any other way achieving tasks such as filtering certain partials of the sound without distorting its transients? Would filters that work in time domain do that instead of FIR filters?
I'd say your best bet would be to use the Spectral Repair features of Izotope's RX package. Unfortunately, if you're filtering any sound you are inherently likely to introduce artifacting of some sort; how much and how noticeable this is will naturally depend on the frequency components of that sound, and what / how much you're filtering out.
RX generally does a pretty tidy job at allowing you to filter out specific parts of the frequency spectrum without 'damaging' the sound too much, so is worth a look if there's some specific audio you're trying to fix.
Eq's introduce phase rotation effects , maybe you could hack your way with digital linear phase eq..
But after all its a certain sound you are eqing , if there are unwanted artifacts in a transient well the transient will be damaged.
There are also multiband compressors like c6 which act very much like an eq but with dynamics