Admittedly, there's different ways to consider this "top 3"... I could look at it like my favorites in each era, which would be:
PG: SEBTP (not only the best IMO but also the first PG era album I got for myself)
PC 70's: ATOTT (probably just cos it has the most 70's era songs I like-Dance on a Volcano, Squonk, Robbery, Assault & Battery, Los Endos)
3 Piece: WCD (it was the first Genesis album I got after first becoming a fan-my mom gave me her copy, and I remember listening to nothing else that whole summer of 1994. Plus it sounds so different from anything else they had done)
If we're talking about which ones I'm "into right now" which as with many of you changes over time, I'd say:
1. ATOTT
2. The Lamb
3. ATTWT
But ultimately my "staples" are what I had mentioned before, which seem to always be towards the top:
1. WCD
2. ATOTT
3. Shapes