I have ALL my MP3 files stored in the following file tree:

C:/MyMusic/MP3/Artist/Album

I want to apply MP3Gain "album mode" (same relative volume from album to album but maintains the dynamics within each album) to all the files. Can I just select the MP3 folder and analyze/gain my whole collection simultaneously rather than doing each album separately?

I have heard that it treats each folder as a separate album but just wanted this clarified before I go ahead with it. I have 100s of albums so I am thinking if possible it will be best to run this overnight?

Yes, it works.
I ofeten use mp3gain in this way, with dozens of albums.
Check options/add subfolders , or you don't see your files.
And, if you are unsure, make some test before.
Enjoy!

Will work good. Remember though that if you use e.g. "Target volume 89", it still can happen that some songs are clipping. If you don't want that you should correct that manually, afterwards, per album.

Geebee