Why do the Sony PCM-D1 and Zoom H4 microphones look like some
sort of sci-fi phaser gun?

Intro

The microphones in the Sony PCM-D1 and the Zoom H4 are fixed in what is known as an x-y stereo configuration, where 2 microphones are placed at roughly the same point and angled at approximately 90° to produce a stereo image.

Stereo Imaging

A stereo image is the illusion of spaciousness created when a recording is played back through 2 speakers. A good stereo image is one in which each instrument or voice has a natural size and a stable, specific location.

The main factors that establish the image are the relative strength of an instrument's sound in each speaker, and the relative timing of the sound's arrival at the listener's ear.

In a studio recording, the stereo image is produced artificially. Each instrument has its own microphone and the various signals are balanced to suit the taste of the producer. In a live recording, where the goal is to capture the energy and atmosphere of a "real" performance, 2 microphones are ordinarily used, one for each speaker.

X-Y Configuration Advantages

The stereo image resulting from an x-y configuration isn't very wide, but it allows for relatively close miking of a sound source and maintains a high degree of mono compatibility -- important if you ever want to ever want to mix your 2 channel-recording into a monophonic signal or broadcast your recording over the radio.

With the x-y and other coincident (same point) stereo setups, you also avoid phase problems that can arise when there is a large distance between 2 microphones. In such a case, it is very possible that one instrument's sound could reach each mic at a slightly different time (sound travels at 1100 feet per second). This difference in time causes a phase shift between the 2 stereo channels, which causes problems when the signals are combined. The result is an uneven, almost shimmery sound.

The coincident stereo techniques avoid this phase problem by mounting both mics at approximately the same point.

That's a long way of saying that it looks that way for a good reason -- and it looks cool too.