Yoshi's pack is aimed at console emulation, while BAFelton's StartKit has a wider variety of emulators (namely, those aimed at computer systems). The StarterKit also includes a firmware update (in case you need it) and a small selection of useful Apps and a copy of 'Timidity' (which is somewhat strange, as I don't think Timidity is used by any of the packaged emulators - Timidity is a sort of midi/sound emulation-thingy that is used by several game and app ports to get around the Caanoo's lack of the proper kind of sound hardware).
I like Yoshi's for the Fact Sheets - it's worth the download just for that, even if you stick with the Starter Kit. I like the "completeness" of the Starter Kit, too. I don't think it matters which way you deploy them if you decide to go with both, as one doesn't have newer versions of any of the emulators over the other (at least, not as of today...). Just my opinion, but I would dump the Starter Kit on first, to get the right folder structure (and update your firmware if you need it), then delete the firmware update files. Next, I'd copy over all of Yoshi's pack, ignoring any duplicates. Then delete the "caanoo_release" folder and "caanoo_release.ini" file - these are for DrPocketSnes, but Yoshi was kind enough to include both versions (fast and compatible) in seperate folders and ini's, so that you can run either one straight from the menu. Also, you can delete "caanoo_hugo" and it's ini file (these are duplicated in "hugo").
However, since both are slightly behind, you'll probably want to update a few of the emulators on your own. DrSMS is now aat v3, and I believe OhBoy has an update as well. Outcast (Atari ST emulator) was fully ported to the Caanoo (the version in StarterKit is a Ginged version, originally for the Wiz). I'm sure other's have updated as well. Check OpenHandhelds