I've read that it might be possible to use YSMenu on clone R4 cartridges.
(things such as the R4 Deluxe, R4 III, R4 SDHC... etc... etc... I'm not going to list them all here)
To do so, you would have to create the YSMenu firmware so that it loads after your "official" firmware has loaded.
In other words, create the YSMenu firmware so that it loads as a moonshell replacement or as a .NDS file... both of which you would launch manually.
I'm not offering any support for it here (I don't have any clones to test with), but it's an option to get better game compatibility, etc.
You can find our thread about generating YSMenu and using it on the R4 here:
viewtopic.php?f=16&t=1957If some of you clone users would like to step up and figure out the ins and outs of using it, feel free (and post your findings here!)

If you are using a2h's software, you'd want to make either the multimedia or file browser version of YSMenu.
If you are using Maikel's R4YSAuto method, ising the
YS_CONFIG_ENG_MNSHL_REPLACEMENT.zip and the
YS_CONFIG_ENG_NDS_FILE.zip configuration files attached to the bottom of the first post would yield the necessary builds (or, use options
3 or
4 if you are manually running the
r4.bat. Option
2 isn't recommended).
Good luck.
Users have posted their experience here:
viewtopic.php?f=50&t=3144&p=19143viewtopic.php?f=66&t=3231#p19441There's a guide and thread, found by user Mazinkaiser, over on the GBATemp forums regarding using custom builds of YSMenu for various R4 clones. You can find it here:
viewtopic.php?f=28&t=2377&start=10#p20924