Something is incorrect here because my X can access the market just fine over WiFi (when I did a hard reset after receiving the 2.2 OTA update, I just sat there at home and reloaded all the apps again very quickly using WiFi).
Also, all the apps I have that connect to the world all work through either 3G or WiFi, whichever is on. I believe WiFi for data takes precedence over 3G when you are connected to a network. So at home I turn WiFi on since I have my router on but at work it's 3G since I can't connect to my company's wireless network.
That does not mean some apps aren't written to use WiFi. There may be some. However, all the apps I have appear to function on both 3G and WiFi and are clearly working on WiFi at home just fine. They just do by default and I did not change anything specifically to change this behavior.
So, you may have a setting wrong or you may not actually be connecting to WiFi (are you experiencing the "connecting...disconnecting" WiFi issue? If so, you may not actually be connected so the apps are defaulting to 3G). If the wireless icon is showing, you should be using WiFi.