I can't run games with unsupported mappers (e.g. MMC5 in Castlevania III US, or VRC7 in Lagrange Point) but other than that I haven't seen any problems. I mean, other than graphical problems that normally appear in NES games. Sprite flicker, scroll seams, etc. What games had glitches? (I could try them out.)
I did have a problem when I tried to make an MMC3 ROM using the FamiTracker driver. The sound went broken after a while. This didn't happen on emulators, but I did get weird non-firing IRQ issues on emulators (I tried to disable any FamiTracker APU writes to 4010/4017, but that didn't help). Not sure if this is a problem with PowerPak's MMC3 implementation, or maybe there actually would be real conflict. I gave up and tried other mappers (VRC6 worked fine, no mapper worked fine). I've seen no problems so far with MMC3 games I'm familiar with (Super Mario 2 / 3, Bases Loaded 3, etc.).
There's an MMC5 mapper implementation, but it's listed as "buggy" on the PowerPak site. If you take a close look at the incompatibility list EVERY MMC5 game is on there.
I've tried a few MMC5 games on PowerPak (e.g. Castlevania III). None of them even boot.
There's only about 11 MMC5 games anyway, and the most popular one (Castlevania III) has a VRC6 version (also there's a translation patch), and it's a rather complicated mapper, which I guess is why it hasn't been finished yet.
rainwarrior: I can't think of any reason it won't work with MMC3. If you have IRQs enabled then it might be important to read $4015 each video frame since the APU generates IRQs. Or maybe it's possible to turn off, I haven't messed with that myself.
jsr: I couldn't think of a reason either; I found in an emulator everything was fine, except the scanline IRQs wouldn't fire sometimes if there were active while FamiTracker was executing. I tried to trap it in the Nintendulator debugger, but didn't have enough patience to figure it out. When I moved it to the PowerPak it would run okay for a bit then eventually bug out. When I have time later I can put together a simple ROM w/source that you could look at if you're interested. I'm not too concerned about it, though. NSFs and other mappers seem to run fine, and I don't have any specific need for MMC3 (it was just convenient for the graphical things I was trying).
Tech: the same mappers are usually hard to implement regardless of platform.
Alllright. I did the audio mod and it seems to be working fine. I used a 100k pot so I could adjust the volume with a knob, and put in a little switch to disable the mod entirely.
I've tried VRC6, FDS, and 5B games. They all seem to be working fine
(though I am really glad for the volume control for non-VRC6 expansions). There's no VRC7 or MMC5, but I haven't tried Loopy's experimental mappers.
Also: if you haven't soldered in a while, it wouldn't hurt to practice a little first.
Me, I'm having ~J-@D!~ do the pot mod for me next weekend. He proposed himself before I even bought my NES & Power Pak, which made me quite happy as I know nothing about soldering (and I get to see James again which is great).
Sidenote: it looks like the NSF player handles NSFs with raw PCM pretty awkwardly. Some don't load at all (I get a blank screen after about 20 seconds of "Loading NSF", and when it does load, the Select button does nothing (instead of bringing me back to the file browser). Does this happen to any other Power Pak owner?
I wonder if 5B audio will ever be available, too (in the NSF player, that is).
Raw PCM can work okay, but a lot of people who use raw PCM make very large NSFs, and there's a size limit on what the PowerPak can handle. (I think the limit is 256k for NSFs, but 512k for regular ROMs.)
I've tried Loopy's experimental mappers; no MMC5 audio, but Just Breed and Castlevania will boot just fine. I think the colour palette in Just Breed is a bit messed up, but I'm not sure.
) 
, and when it does load, the Select button does nothing (instead of bringing me back to the file browser). Does this happen to any other Power Pak owner?