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Edit: I re-evaluated this answer for version 1.0.2 - the results have changed slightly. I also added cost considerations to the answer

With version 1.0, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.

As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.

Antenna     | Mass | Cost |Energy | Time
------------+------+------+-------+-----
16          | .005 | 300  | 1200  | 60s
DTS-M1      | .03  | 600  | 1200  | 35s
88-88       | .025 | 1100 | 2000  | 10s

As you can see, the antennas later in the tech tree have a higher transmission speed. The fastest antenna - the 88-88 - requires more energy than the other two to transmit the same results.

Often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the 88-88, you need more battery capacity and/or a lot more energy sources which means more mass to carry.

That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice because it has the least mass and is the cheapest.

The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver.

By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.

Note: With Version 1.2, the functionality of antennas was changed a lot and more antennas were added. This answer might not be very useful anymore.

With version 1.0, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.

As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.

Antenna     | Mass | Cost |Energy | Time
------------+------+------+-------+-----
16          | .005 | 300  | 1200  | 60s
DTS-M1      | .03  | 600  | 1200  | 35s
88-88       | .025 | 1100 | 2000  | 10s

As you can see, the antennas later in the tech tree have a higher transmission speed. The fastest antenna - the 88-88 - requires more energy than the other two to transmit the same results.

Often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the 88-88, you need more battery capacity and/or a lot more energy sources which means more mass to carry.

That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice because it has the least mass and is the cheapest.

The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver.

By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.

With version 0.23, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.

As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.

Antenna     | Mass | Energy | Time
------------+------+--------+-----
16          | .005 | 1000   | 45s
DTS-M1      | .03  | 1500   | 30s
88-88       | .025 | 2000   | 15s

As you can see, the antennas later in the tech tree have a higher transmission speed, but at the expense of a lower energy efficiency. But often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the faster antennas you need a lot more battery capacity and/or a lot more energy sources which means more mass to carry.

That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice. It has the lowest mass and needs fewer additional mass in form of batteries and solar panels to operate fluently. That means it is the most economic method to transmit your research results.

The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver. By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.

Edit: I re-evaluated this answer for version 1.0.2 - the results have changed slightly. I also added cost considerations to the answer

With version 1.0, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.

As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.

Antenna     | Mass | Cost |Energy | Time
------------+------+------+-------+-----
16          | .005 | 300  | 1200  | 60s
DTS-M1      | .03  | 600  | 1200  | 35s
88-88       | .025 | 1100 | 2000  | 10s

As you can see, the antennas later in the tech tree have a higher transmission speed. The fastest antenna - the 88-88 - requires more energy than the other two to transmit the same results.

Often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the 88-88, you need more battery capacity and/or a lot more energy sources which means more mass to carry.

That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice because it has the least mass and is the cheapest.

The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver. 

By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.

When it comes to electricity use, the first antenna, the Communotron 16, is the most efficient one. It is also the one with the lowest mass by far.

But when it comes to speed, the Comms DTS-M1 will transmit your research results faster than any other antenna. There are, however, few situations where transmission speed is essential. Usually the limiting factor in sending large amounts of research data is the energy supply. One case where it might matter could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver. By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.

The Communotron 88-88 is the one with the highest energy consumption per Mit while being in between the others in transmission speed and being only slightly lighter than the Comms DTS-M1. That means that it is usually a sub-par antenna which should be avoided. Its fold/unfold animation looks cool, though.

For most situations I would recommend the Communotron 16.

Source for antenna stats: http://wiki.kerbalspaceprogram.com/wiki/Antenna

With version 0.23, the antennas were rebalanced. But the stats listed on the construction screen seem to be misleading, because they have little relation to their actual performance.

As an experiment I tested transmitting the atmospheric analysis experiment with each antenna and measured the energy and time (without unfolding animation) it required.

Antenna     | Mass | Energy | Time
------------+------+--------+-----
16          | .005 | 1000   | 45s
DTS-M1      | .03  | 1500   | 30s
88-88       | .025 | 2000   | 15s

As you can see, the antennas later in the tech tree have a higher transmission speed, but at the expense of a lower energy efficiency. But often the limiting factor when transmitting is energy supply, not transmission speed. To really make use of the faster antennas you need a lot more battery capacity and/or a lot more energy sources which means more mass to carry.

That means when timing is not a concern, the first antenna, the Communotron 16 is usually the optimal choice. It has the lowest mass and needs fewer additional mass in form of batteries and solar panels to operate fluently. That means it is the most economic method to transmit your research results.

The only case where it might make sense to choose a faster antenna could be a probe which is planned to research the lower atmosphere of a planet but isn't equipped in any way to slow its descent and thus only has a limited time before it crashes onto the surface performs a lithobrake maneuver. By the way: When you equip your craft with multiple antennas you can transmit multiple results in parallel which saves you a lot of time.