For the ISA bus: - Tseng Labs, Western Digital (WD), late model Cirrus Logic cards
For the VLB bus: - S3, Tseng Labs, Cirrus Logic
For the PCI bus: - S3 (Trio64, Virge), Cirrus Logic (late models), Matrox Millenium series, Tseng Labs ET6000
For AGP: - S3 (Trio 3D/2X, Virge, Savage), Voodoo (Banshee, V3), Matrox (Gxxx series), early nVidia cards - Riva 128, Vanta, TNT (except the TNT2)
I have little experience with ISA bus cards, but I've used Tseng ET4000AX and WD cards in my builds with great results. Late model Western Digital cards are as fast as TSENG cards and quite a bit cheaper (I've seen some silly ebay prices for tseng cards).
On the PCI bus, Matrox cards are possibly the fastest you can get, but compatibility with some dos games is lacking. That is why I prefer S3 cards. Similar performance, great compatibility. Cirrus Logic cars have great compatibility as well but they are slower than both S3 and Matrox cards. In my opinion, the S3 Virge 4MB makes the perfect PCI card. Fast, great compatibility. You can also use PCI Vodoo cards (Rush, Banshee, Voodoo 3) - but please note that the Voodoo Rush's Alliance 2D core has some compatibility issues with some '89-95 DOS games (Jazz Jackrabbit comes to mind here).
AGP is a different story. If you're building an AGP rig you will want both DOS and Windows performance - so I recomend Voodoo cards - perticularly the Banshee and Voodoo 3. Great DOS performance and compatibility, great 3D + Glide! S3 cards have great DOS performance and compatibility but except for the Savage4 and Savage2000, they have extremly poor 3D performance. The Savage4 and Savage2000 perform quite well in 3D (the Savage4 16MB in my collection slightly outperforms the G450 dual-head in most games I play). S3 3D drivers are a bit sketchy so beware. Matrox cards are someware in the "awkward valley". Great DOS performance and image quality, but sketchy compatibility... 3D performance is on par with late S3 cards and some nvidia cards (G450 ~ TNT2). I can only recommend S3 or Matrox AGP cards if you plan to use a PCI Voodoo card or V2 SLi build.
Most nVidia cards have issues in DOS. They are quite fast - sometimes too fast for some dos games. As such, anything faster than a TNT will have issues playing games like Crusader: No regret, Descent, Supaplex, Golden Axe and others (stuttering, corrupted textures, etc). Early cards like the Riva 128, TNT(1) and Vanta work great in DOS.