My personal opinions (I'm going for price-performance here):
ISA: Tseng ET4000AX. It was fast, compatible and for the longest time quite plentiful. Some very old games had quirks with them though (Tank Wars by Kenny Morse had difficulties showing some of the icons, but that was a minor glitch). Some later WDC chipsets were pretty good too (though early Paradise chips were dogs.) Third would be Cirrus GD5426+ as DOS was not dramatically slower and the accelerator made Windows more bearable at least.
VLB: Cirrus were super-common and strictly average in all areas, though 5429 was a little better. S3's 64-bit Vision and Trio series rules the roost for overall DOS and Windows performance per dollar, as long as they were equipped with 2MB or more of memory. 805 was okay, but only just (they tended to be visibly faster than Cirrus's in Windows, but also visibly behind in DOS.) Some later Trident cards were surprising though: 9400CXi for instance had remarkably fluid Mode13h response for a Trident, and 9440 was decently quick for the price. (Trident of course tended to suffer from monitor detection troubles, as mentioned earlier.) Also surprising was an Avance Logic 2222VL - while its Windows and VESA VBE speed was nothing to write home about, it was very capable in Mode13h at least.
PCI: Many good chipsets, S3's Vision and Trio series were plenty competitive overall and were common as heck, often quite cheap too. ViRGE was pretty decent, but Vision/Trio usually were noticeably faster in pure DOS. Trident's 64-bit TGUI9680 was a surprise as it was quite strong in DOS (especially Mode13h), though the VBE remained mediocre at best. 3dfx Banshee and V3+ of course dominated the whole field, but were often much harder to find and pricier, and some 486 PCI boards weren't too thrilled with them. Didn't use a Matrox too much sadly, but I remember owning a Millennium 2 based card that didn't really seem any faster than my S3 Trio64V+.
