There are a few high quality games which have both DOS and 9x versions. To sample those with excellent graphics and sound, I would include Quake, Hexen 2, Hind, and EF2000. EF2000 has been discussed in other threads, a highly rated game, while Hind has been less noticed. Hind is available from gog.com and its graphics in DOS are comparable to the early directx games in Windows, and in addition has received highly favorable reviews. It's been suggested that Hind demands a joystick and throttle device. These two simulation games show the furthest reaches of DOS game engines.

The DOS version of Quake runs well in DOSBox, but there is a project which maintains compatibility with this version yet adds bug fixes and some enhancements, especially to the user interface. It is called the Quake Info Pool project (QIP). The DOS, 9x, and GL versions of QIP quake are available as source and binary code. I was surprised at the good performance in this version of DOS Quake, the VESA modes are playable. The GL version in DOSBox/9x also showed good performance; however, in both versions the bug fixes are worth the download.

For the QIP DOS version, there is a way to modify the water so it appears transparent, although the water surface itself will not be seen and also the lava will appear transparent. It requires Dr. Spalt's Transparent Waterhack which runs against BSP files. The BSP files must first be extracted from the maps in the .PAK files via a tool.

Hexen 2 is a Windows game. However, there is a DOS port thanks to the Hammer of Thyrion project (HoT). The DOS version features a software renderer with excellent features and high quality textures. I don't recall a better software renderer in a fps game, DOS or Windows. Moreover, the framerates are high, similar to DOS Quake, and allow fast framerates in a slower Core2Duo system (regardless of GPU) at 640x400 resolution. It requires a download; (HoT H2PATCH.EXE) patched PAK0.PAK, PAK1.PAK from your installation of Hexen 2; and optionally the music files. The DOS version does not support MIDI formatted files, but the OGG and MP3 format is supported (I haven't tested the CD audio option as discussed on the Steam forums). One way to create music files is to convert the CD audio tracks on your Hexen 2 CD-ROM to MP3 files and place in the MUSIC subdirectory; these files are renamed according to the MUSIC.TXT documentation (for example, track02 -> casa1.mp3). In game, there is an option under music for "all codecs", allowing support for OGG and MP3 music. For networking, IPX is reportedly working for this version and the expansion pack should be compatible with this project. Configure the dosbox configuration file so at least 32mb of RAM is available, in any case.

Both QIP Quake and HoT Hexen2 support the higher VESA resolutions (1280x1024 in default dosbox). Supposedly, the HoT Hexen2 version has support for even higher VESA modes.