I still do it, mainly because Wii64 for me had worse slowdown than the VC emulator.
I haven't been extensive though. I injected Master Quest into the normal Ocarina of Time, and a hack of Super Mario RPG into Super Mario RPG, so mostly games that are modified versions of the original game being emulated.
You may still wish to try Wii64 though. Most people consider rom injection to be very hard.
Also, a few titles, DK64 comes to mind, I haven't seen emulated properly with injects OR Wii64.