Thanks for the advice... I opened up the BAED ISO and it looks as though I might be able to change the emus that are there. It appears on the surface to have a call structure that would make that possible if I don't change the dir tree names. If not, it also appears that some of the source code is there, and if I can locate a copy of the XDK (yeah, right) then I can make it work the harder way.
I'm not sure I see the functional difference with having the emulators on HD and the ROMs on DVD. Either way it's going to load the entire executable into memory. The emulators do appear to have defaults for paths to spots on the HD for config files, saves, etc. They appear to be configurable, too, so they can get moved around some. I'll try your recommendation and see if it makes a substantial difference. N64 is one of the systems I don't really need emulation for as we still have one in the living room that gets regular use (and about 5 more in the basement).
I was a console collector for years, so for me, emulation is really just a bit of convenience. I still own multiples of almost all consoles and many of them own half or more of the domestic libraries.
Apologies for being absent for so long. I am a WoW addict, so virtually all my free time is spent there lately. =)
Other than possibly MAME where the roms change, the emus are easily swapped out and changed if they are on the HDD, but you don't have to worry about re-burning CDs/DVDs for your roms. I find that if I hear about a new emulator for one of the systems I like to try it out and see how it works out. You may just want to get the current best and not tuch it again, so that's fine as well, just wanted to clarify where that recommendation comes from.
Or you can just cave like I did and buy a big HDD to put it all on.

As far as the N64 stuff... yeah, I understand. It's all about convenience for me as well, though it sounds like my library isn't as extensive as yours. I no longer own a (working) N64, so that's my draw there.
Oh, and for what it's worth... I messed around with some of the netplay functionality once in (I think) FCEUltra and it was compatible with the PC version's netplay settings. It was a fun proof of concept, and if I ever have multiple cabs with an xbox in it I might set it up so you can play them against each other. Could be fun.
I've not tried the SMB sharing stuff, but I hear it can be very nice if setup properly. SMB and I don't like each other, I've ended up with ccxstream for videos on my PC -> XBMC which works well.
Let us know how it works out.