I like the Pi and it's cheap fun but it's not the best hardware for emulation. On the Pi I store small uncompressed roms locally (SD card) and access larger roms from my media center so space isn't a Pi issue for me. I honestly don't play much on the Pi because my media center and arcade cabinet are much more capable. That being said I use Windows mainly because some emulators aren't available for any other OS and it also has the largest selection of frontends.
In terms of the Pi, you are correct in saying .pbp is the best compression option for PS1 games using Psx-Rearmed. The Pi can use .chd files for some of the other systems I mentioned.
I've been gaming for a while and have a lot of roms. If I were to start today knowing what I know now I would get all my roms from a current MAME set because it has every game with checksums to know they are correct. Now that MAME is merged with MESS a complete rom set is close to 3TB but includes just about everything that can be emulated except GC, Wii, PS2 and PS3. MAME games are already compressed and ready to use in .zip, .7z or .chd formats. You can use these games with other emulators too, not just MAME and you can get the pieces you want without having to download the whole thing. If you take this path this thread might be helpful
http://forum.attractmode.org/index.php?topic=2307.msg15606#msg15606.
Like most of us, I didn't get my roms like I mention above. I have uncompressed, converted and compressed most of my files more than once over the years. Here's some simple .bat files you can create to automate the process. Create a text file, copy the lines listed below into it and rename it. Place the .bat file and the corresponding .exe into the folder with the roms you want to compress and run the bat file. The .bat file will look in subdirectories and compress anything that matches the file extention. It will leave all your existing roms untouched, you can manually delete them if you're happy with the results. FWIW - All the tools (.exe) I mention below are free.
Any file extention to .zip (I'm using 7za.exe for these)
nes2zip.bat
for /r %%i in (*.nes) do 7za a -tzip "%%~ni.zip" "%%i"
pce2zip.bat
for /r %%i in (*.pce) do 7za a -tzip "%%~ni.zip" "%%i"
sms2zip.bat
for /r %%i in (*.sms) do 7za a -tzip "%%~ni.zip" "%%i"
Any file extention to .7z (I'm using 7za.exe for these)
nes27z.bat
for /r %%i in (*.nes) do 7za a -t7z "%%~ni.7z" "%%i"
pce27z.bat
for /r %%i in (*.pce) do 7za a -t7z "%%~ni.7z" "%%i"
sms27z.bat
for /r %%i in (*.sms) do 7za a -t7z "%%~ni.7z" "%%i"
Disc based systems can be converted using chdman.exe (chdman.exe is included with the MAME emulator, newer versions have the best compression). FWIW - To convert to .chd your existing audio files can't be compressed (i.e. no .mp3 audio files) they need to be .wav or possibly another uncompressed audio format.
convert2chd.bat
for /r %%i in (*.cue) do chdman createcd -i "%%i" -o "%%~ni.chd
for /r %%i in (*.gdi) do chdman createcd -i "%%i" -o "%%~ni.chd
PSP and PS2 games like the .cso format and they can be converted using maxcso.exe (get the latest version for best results)
iso2cso.bat (for performance adjust the thread count for your system, since these files are large too many threads could cause unresponsiveness or overheating (i.e. adjust or remove the thread statement all together but expect for your system to be taxed to the max if you do))
for /r %%i in (*.iso) do maxcso "%%i" --threads=2 -o "%%~ni.cso
Hopefully these will be helpful to compress your rom sets. You can obviously edit them to suit your needs but this should put you on the right path.