I uninterestingly use the default installation path & folder name for anything I install...except, well, padding those below th10 with a zero to align them nicely, like Watermelonz's. Everything goes to Program Files folder, just for me liking consistencies.
The part where I get a bit sort-creative though is in their shortcuts.
Normally, in Win98, I rename them to, for example, "TH07 Youyoumu ~Perfect Cherry Blossom~", then its respective "th07 config" in their dedicated "config" folder. With our system being WinXP now, implying it can now read Unicode characters, I name it in the same format, except the English being their Japanese equivalent, if applicable.
I like the numbering prefixed instead of eliminated for easy sorting. It also serves as some kind of progress-tracking device, tracking how much games of the series this one-man developer has accomplished already. =w=