That's a tough choice. There are quite a few more GOG games I adore (~20-30), and that's not even counting new favorites I haven't gotten around to playing yet. That said, these may not be my definite top 5, but merely a good approximation. Actually, I'm going to cheat a bit here and list my top games in my top (sort of similar) genres.
Descent 1+2/WC: Privateer - Loved them when I first played them, and they're still a blast to play. The latter is sure is showing its age, but it's still my favorite space sim.
Master of Orion 1+2/Alpha Centauri - They definitely tie for my favorite 4X games, bar none.
Original War/Stronghold - My enthusiasm for everything RTS may have left me long ago, but these are damn good enough for me to still love them despite that fact.
Crusader: NR x2/Blake Stone x2 - Dated, awkward controls and all that they may have, but their wonderful mindless action can still be a great joy nonetheless.
RollerCoaster Tycoon 1-3 - I've been a big fan of Theme Park back in the day, and these are just as good if not better - though I did like the full simulation aspect of TP with stocking, contract negotiation, park sabotage. I know some don't think 3 as that great, but it's different and RCT enough for me to love it just the same. As trivial as it may seem to some, I find that being able to fully ride each and every attraction is very enjoyable.