Why do some 2 seat fighters have side by side seating, while others have the pilots inline with each other? In some multi seat fighters, like the F-111 Aardvark the pilots sit next to each other, like so:



While in other multi seat fighters (most of them it seems) the pilots sit with one in front of the other, like this F-15E:



Why do some fighters have the pilots in a line like that?  Is there an aerodynamic or performance advantage that comes with having them in a line?  Or maybe it's so they can have a bubble canopy, which perhaps affords a better view? It seems it would be easier to work together when they are side by side.

So why do some multi seat fighters have side by side seating, and others are in a line?
The tandem arrangement (one behind the other) is used on aircraft that have single seat variants. The F-15, F-16, and F/A-18 are all primarily single seat aircraft. It's much easier to stretch the nose out a bit to add a second position than to make it wider. This arrangement is also more aerodynamic, requiring less frontal area.

Fighter aircraft designed for a crew of two will often choose the tandem arrangement for aerodynamics. If both seats need forward visibility, there are compromises available. Some aircraft like the F-15E can be flown from both seats even though there is less visibility from the back. It's possible to have a bubble canopy in side-by-side configuration (this is particularly seen in aircraft kits), though it will create more drag than a tandem canopy.

Having the crew sit next to each other can be helpful for crew interaction and sharing instrumentation. The F-111 is one such special case:


  The USAF wanted a tandem-seat aircraft for low-level penetration ground-attack, while the Navy wanted a shorter, high altitude interceptor with side-by-side seating to allow the pilot and RIO to share the radar display.


This may have also been easier to design the escape capsule. Of course the Navy changed their mind and went with the F-14 instead for better maneuverability.