Archival and day to day use do differ.
7zip is noted as supporting cross file compression, classic one in the case of ROMs being you put all the regions, v1.1 and whatever bad dumps, hacks, betas and more you collect into the same file. It compares them all, sees where they match and does not replicate that multiple times in the compressed file. Now takes several times longer to decompress. You do that for a system and you can do very well above and beyond even the previous thing. Now takes possibly minutes to decompress a few megs of ROM. Very annoying compared to plain ROMs or simple compression, not to mention many emulators if they support compressed ROMs out of the box will only do it for single ROM or first ROM in archive which means you then are obliged to use a manager. There is also the problem that corruption in the large archive of everything might tank the lot, corruption in an archive in a directory of them means future you gets to go to a ROM site and download that one again. Also adding files if a new dump appears is annoying if you have to unpack and repack the lot to do it properly.
After this we get to talk about the less clear cut cases. PS1 games fairly often used CD audio, many then took to compressing them (40 megs per 3 minute track give or take, down to a tenth of that if you use basic MP3 of reasonable settings and even less if more modern) and thus saved dramatic amounts of space.
PS1 also throws us a curve ball in the form of lack of Scene standards at the time. Consequently the dumps of the day might be in a thousand different formats where more modern redumps (which some hackers prefer for ROM hacks) might be standard bin-cue.
Wii scrubbing did represent something at one point. Today you can regenerate from almost any common format (normal, scrubbed, mega scrubbed, WBFS...) so there is that.
The original xbox has some concerns here. Many of the dumps made at the time were additionally compressed and items lost beyond what the devs left in there in a bid to get file sizes down. Fine for the original xbox but come 360 DVD mods trying to do backwards compatibility with the xbox and you needed 1:1 original (or near as)
DS has a few ones here. Most notably all the later redumps you might see are from when an older dumper by Rudolph assumed an area of the header was blank, as indeed it was at the time it was made. Said area got used for some info in later games to allow the DSi to work with its additional security. However no DS original flash cart cares, no DSi capable flash cart cares, no DSi hack cares, no DSi emulator cares and never will unless someone deliberately programs in extra security that nothing cares about...
To that end figure out how much ROM hacks mean to you (there are ways if you are even vaguely capable of making things work without the suggested ROM) and from there choose your formats accordingly (alas there is no real answer there as some hackers will go for Scene original, some will go for no-intro or some dat set and some will go for something basically as the end user will rip it as naturally everybody owns the game and has ripping gear if they are playing in these circles).