i second the TL866 series. It does most 27 series 42 pin chips with no issues including the 27C4096.
if you have the older "866 mini" version, 27C160 or 27C322, or the TSOP 29F016 or 29F032 on a TSOP adapter board, you need to use an adapter to swap out the memory banks to write them. it does support those 4mb versions of the chips, so you just break up your rom into 4mb chunks and swap the A18 and A19 write banks... and will do up to 16mb chips this way.
i'm not sure if the newer B or CS versions have fixed this issue or not, but if you need to do 8 or 16mb chips, you can.