Blitzkrieg is another computer war title that uses supply lines. Combat is focused on the units (no bases) so managing a supply truck doesn't get in the way. On the map there are several fixed supply crates. Any units within range will rearm. When attacking another point on the map, a supply truck must drive to a controlled supply crate, load up, and drive back to the unit (mostly tanks).

It has been awhile since I played it but I believe the ground units (soldiers) were exempt from needing supplies and only the bigger units (tanks and such) needed supplies. I can't recall whether or not you could destroy the supply crates but you could destroy the supply trucks.

Closest thing you can do in Civ4 is to just spread a billion units over the enemy's territory after you've pillaged their road/irrigation/mining/resource network into oblivion. It's not really a supply LINE, but it has the same effect if you destroy it.

To be honest, I can't ever recall a single game using them. Total War really doesn't use supply lines, at least as of Medieval TW; you could starve out castles under siege, but there wasn't any real lines of supply.

I've worked on occasion on a Civ-type game, which would include logistics as a tech, but everything was automated. Each unit had an invisible route mapped by the system to the nearest allied city or fort/base. If that line had an enemy unit placed on it or adjacent to any of the tiles it crossed, it was compromised and the unit would take damage until it was re-established or the unit destroyed.

It's not well fleshed out because I've only barely worked on the TBS idea here and there; it just popped in there.