First, and definitely not the worst, I highly suggest VOGONS! I use this website quite a lot for my vintage computing needs.
Secondly, take a look at 3D Realms. This is their official website, I like visiting the old one too. I downloaded some patches for games like Shadow Warrior on there a while ago.
I also like visiting Digital Press sometimes. It's mostly retro console stuff, not much PC stuff.
Looking and reading at obscure, vintage computers on oldcomputers.net is also a lot of fun when you have some time to kill.
Do you want to play some MS-DOS games, but you don't have an older computer? Well download DOSBox, and then head over to My Abandonware and pick up some MS-DOS games...for free! Virus free, too! (Disclaimer: This isn't considered pirating by law, as pretty much all of the games on here have developers and publishers which are LONG gone.)