I loved Into the Renaissance when I first played it, but then I saw a really big problem it had: too much empty space in Central Europe and the Balkans. Granted, it was a G&K scenario, meaning no Poland that could take up some space there - but even a bunch of new, scenario-unique city states would be nice. Or even a civ or two adapted from regular ones just with a new icon and/or static leader screen, for example for Poland and Hungary. ItR deserves a Deluxe version, with BNW civs and mechanics included, but I still like it.
I played Scramble for Africa twice, and liked it very much. It provides very dynamic gameplay with a lot of things going on - colonisation, exploration, digging, fighting, building railroads etc. Very fun.
Among the rest, some are memorable, and some are not. If we're into lists, I'd put mine in such a way:
1. Scramble for Africa
2. Into the Renaissance
3. Conquest of the New World Deluxe
4. 1066 - fun, nail-biting scenario
5. Fall of Rome - same as above
6. Wonders of the Ancient World - I hoped a dual-civ DLC would accompany this, with Hittites and Sumer making an appearance
7. Empires of the Smoky Skies - love the setting, but the scenario underdelivers.
The remaining few have aged badly (Mongols), or are really boring (American Civil War). Samurai Invasion of Korea still holds up, but I wish it could use the 100 hit point system.