I'll usually just count the number of times I go through a riff before the next change.
If there's a lot of space in the song with long periods of no guitar playing, the drummer usually puts in a fill, or change the hi-hat, or hit a cymbal to signify a change. There's usually something there to key off of.
Once I completely learn a song, I'll just go by feel.
Some of the country tunes I played with my last band gave me fits. On a couple of tunes the song structure was weird, with no chorus, and key modulations that seemed to come out of nowhere. Easy for a country guy to hang with, but tough for someone used to a "verse/chorus" kind of rock format.
Guitars:
Fender 2006 MIM Fender Stratocaster HSS in 3TS
Ibanez RG 570 with a bridge Invader
ESP M II Deluxe with a Tune-o-Matic bridge
Eleanor, the magical, mystical Road Worn wonder Tele
Blackstar HT Club 40