I actually have both Freeciv as well as the open-source C-evo installed on my netbook, since this computer can't play any official version of Civ more recent than Civ II (Civ III needs a 1024x768 screen).
Most of the time, I prefer C-evo when on my netbook, but it has a number of annoyances such as no settler/worker automation nor any real ability to customize the rules. It is a lot more cohesive, immersive, and stable than Freeciv, and has a fun factor Freeciv just doesn't have for me. It's best on a small map to keep the micromanagement down.
Freeciv is a lot more flexible, yes, but its default interface feels like using a spreadsheet and its SDL interface is unstable and buggy. I really wish I had the free time to iron out the SDL client's bugs myself.
One Freeciv advantage over C-evo is that there is a Java utility out there that can convert Civ IV maps in to Freeciv maps, so I can play a Civ4 map I like with Freeciv while traveling on the road.
The best open-source turn based strategy (TBS) game that plays on a netbook is undoubtedly Battle For Wesnoth, but that's not a Civilization-type game.
In terms of commercial games, the best Civ-type game for a netbook is either Alpha Centauri or Call To Power 2. For a turn-based game that's not Civ, Heroes of Might and Magic III is really good, and Age of Wonders: Shadow Magic deserves a shout-out. All of these games are legally available DRM-free for $10 or less at GOG.com.
- Sam