Classic Traveller
This is the only RPG which doesn't allow the player to bypass the mini-game by becoming a passenger, because even as a passenger the PCs' lives are at risk. However, this game also has the most simplified use of the PCs' relevant skills since skill level doesn't adjust the difficulty of the rolls involved.
The Navigation and Piloting skills are written in such a way to suggest that if a character has the skill they simply perform their task without a roll being necessary. Navigation is only difficult and requires a roll when the character doesn't have equipment or computers on hand to assist. Divided up by vehicle type, the character is able to pilot less complex craft based on how high the character's most advanced Piloting skill is.
Traveling from one planet to another in the same system is given a Travel Time table, but there appears to be no need to roll dice for this kind of travel. Interstellar travel also doesn't require a Piloting roll, which is noteworthy. However, two rolls must still be made when a starship jumps from one system to another.
The first roll is to determine if the starship malfunctions. If the ship requires engineers then each one that is missing applies a -1 to the roll, other negative modifiers include using unrefined fuel and overdue maintenance. Under optimal conditions, there is no possibility for failure. If a failure does happen then multiple systems can require repairs (each one is rolled for separately), and if life support happens to be one that goes down and doesn't get repaired, everybody's dead. Joy.
The second roll is to get the starship where you want it to go. While you need somebody with the appropriate Piloting skill to make the jump, their level of skill is not used. The roll has two negative modifiers, one for using unrefined fuel (again) and another for trying to cut the jump close to a planetary body. See, in Classic Traveller your jump drive had to be 100 diameters away from the planet in order to jump safely (to get to this distance is also shown on the Travel Time table provided you know the diameter of the planet you're moving away from or jumping to, but the GM surely would know this even if you don't). This is another roll that under ideal conditions has no possibility for failure.
Being a passenger on a ship is relatively easy, unless you want to save money by traveling in the Low Passage bunks, which is essentially suspended animation. This would require a roll to revive the character where they could potentially die if the roll was failed. The roll could be modified by the character's low Endurance score or the presence of a trained medic.
Stars Without Number
Only the Navigation skill is required to set courses within star systems, and no roll is necessary unless some hazard might hamper movement or the pilot is looking for to shortcut the travel time. To jump from system to system a character needs Navigation at a level above basic proficiency and it requires a roll, modified by distance traveled and how old the navigational star charts are. If the pilot wants to shortcut the time this can also increase the difficulty. Failing the roll leads to a random mishap.
GURPS
This is a difficult rules system to quantify since a GM can houserule so much of it. There are simply too many variables in the GURPS rules to list the requirements for navigating and piloting a starship between systems.
The only science fiction game of GURPS I ever played in was a Star Trek campaign that used a skill-heavy emphasis. The GM of that game required a roll for navigation and a roll for helm, usually the same PC made both rolls. A failure on one roll could result in the ship going someplace we didn't want it to go, and a failure on the other roll could result in a shipboard malfunction. I believe these were custom mishap tables the GM had written.
Star Wars Sage RPG
No skill or roll required to travel from planet to planet, rolls are only required for combat and evasive maneuvers.
Traveling through hyperspace is different, takes a random amount of time modified by the power of the starship's hyperdrive, and requires the Use Computer skill. The difficulty of the check is dependent upon the existence of a navigational computer, access to the HoloNet, and how much time the navigator takes to plot the course. Failure results in a re-roll, if another failure occurs the ship gets randomly damaged and takes twice as long to arrive at the intended destination.
Trinity
There are rolls required for using a starship in combat, or being involved in a chase, but otherwise starship travel is handwaved. There are no skills and no rolls required to travel from place to place, though there are time restrictions based on how powerful the starship is. There are rules for jumping from system to system, or psionically teleporting, but these don't require rolls, they simply give PCs' penalties upon first arriving at their destination until they orient themselves.
I'm partial to the Classic Traveller method. It's the most difficult to explain, but it's the easiest to use since failure only occurs if you're not operating with a full crew or using poor fuel.
