I heard that ATI/AMD cards work worst with free software. 3D acceleration is
unavailable without non-free firmware.
Nvidia cards should work with free driver/firmware, but last generation of
(native) AGP-based Nvidia cards (GeForce FX5x00 series) were much weaker than
ATI counterparts (Radeon R9x00/9x50 sereis). You can try to find a GeForce
FX5900 and see how well it performs. There are also very few bridged AGP
versions for newer cards like Nvidia GeForce 6x00 series or ATI Radeon Xx00
series.
If you really want to build a "retro-PC" with AGP graphics cards, I'd like to
suggest Asus P4P800SE motherboard with Asus CT479 converter board, which
allows you to install Pentium-M processors on desktop computers. Also try to
find a FX5900 card and four 1-GiB DDR memory modules. Above is the best AGP
platform (freedom respecting) I could remember.