This is the "The Bomb" variant my friends and I came up with:
New Rules: Once per round, each player has a Bomb. During his turn, he is allowed to use The Bomb to destroy one piece of track he is connected to. This ability cannot be used the turn he connects to all of his cities. Otherwise, it would be very easy to sabotage one large branch which the player doesn't use before ending the round.
Suggested Rule Change: Alter the line "Players do not actually lay missing track" in the Scoring a round section to read "Players lay missing track, but these are removed before other players score." i.e. If a player starts in Portland and all of his routes go through the mountains to the east, he does not have to lay that double track once for each city. Of course, you probably won't physically lay the track at all, but the rule change is worded so that other players do not use the track you would lay.
Effects on the game: This was introduced as a play balance mechanism. If a player is about to end the round or is perceived to be ahead in the game, the others can more easily level the playing field by targeting his most valuable tracks. It also adds something which the players can bring to the bargaining table. Plus, it's fun to be destructive now and then.
There are also some subtle tactical effects on the game. Double lines are prime targets for The Bomb. Laying "robust" networks becomes a consideration. Where you place your starting position is also more important. In one round tonight, a player started midway between Cincinnati and Memphis (goodness knows why). All of his routes went across the Ohio river immediately to the northwest. That track was bombed 4 times (in a 6-player) game because that was his only connection to the greater network, and there was nothing for him to do but rebuild it every time it was destroyed. For the record, he only lost 5 points for that round because the track he would have built was done by other players, thereby helping him at the same time.
The suggested rule change above is so a player isn't unnecessarily penalized when a track which all of his routes use is destroyed and the game ends before he can replace it. On the other hand, if a player leaves himself in that position, he may deserve everything that's coming to him.
Variants on this variant include "Nukes," where a destroyed track permanently destroyed and cannot be rebuilt. Others versions are minor tweaks such as altering the severity of Bombs (e.g. 2 single-lines or 1 double-line), number available to each player (e.g. giving more to the player who is losing), or sacrificing part of your turn for sabotage (e.g. for each point of track you don't lay, you can destroy 1-2 lines).