What are the community views on Death Rays ...
I would think that Death Rays were not really meant to be balanced. After all, a weapon capable of blowing up a planet through a planetary shield and destroy the planet with a single blast probably has more than enough power to blow through anything you can put on a ship or space station. They require significant amounts of space for both the weapon itself (140 size units) and the reactors to support its energy requirements (400 energy per shot, 47 energy per second - the storage requirement is the issue here, not the output requirement, and while you'll eventually be able to meet the storage requirements with a single HyperFusion reactor, you're still looking at at least two reactors worth of storage for a single Death Ray with anything else). It's also not the most reliably available weapon in the game, its range is somewhat low for a high-end blaster (440 range, somewhat less than the Shatterforce III or Titan Beam II/III, and much less than any but the early torpedoes), and if I recall correctly it's rather inaccurate against ships. While its DPS per unit size is not incredible (1.51 at point blank, down to about 0.5 at 440 range, or comparable to the Shatterforce Laser III and much worse than the Titan Beam II/III), this hardly matters, as I don't think I've ever seen anything survive being hit even once by it. The next most damaging non-superweapon has more than 10 times less damage per shot and additionally takes more time to fire, while the Titan Beam III has a little over 60 times less damage per shot, with a similar damage decay rate when accounting for the shot power difference (60 Titan Beams lose 240 damage per 100 range as compared to the Death Ray's loss of 270 damage per 100 range while having a similar salvo damage to the Death Ray's single shot damage).
... and Area Weapons?
Area weapons aren't really intended for use within fleets, in my opinion. They're more the kind of weapon you put onto a lone tank unit to send in ahead of the fleet and do a bunch of damage, then withdraw that ship as the main fleet comes in to deal with the newly-damaged enemy forces. They're also not meant for one-on-one combat, as they're a low DPS per size unit weapon when hitting only a single target, which makes your current test setup where you spawn a single cruiser to fight a single cruiser not particularly fair for the area weapons. Each level of area weapon is nevertheless a fairly consistent improvement over the previous version, but they need to be hitting at least three targets to have a similar DPS per unit size to blasters. Best use for these really is as a kind of raider that jumps in, fires off some shots into the crowd around a spaceport or something like that, and then withdraws when its shields start getting low, with a fleet of more normal warships or a replacement raider jumping in to continue the attack. It might be worthwhile combining these with the area gravity weapons to clump enemies together.
Personally, I don't use these because they're not a good fleet weapon, and I only really want to manage groups of ships rather than lone attack vessels, and they're not really a good choice for an escort ship.
Anybody using Tractor Beams as part of their combinations?
A tractor beam or two is always helpful on ships whose weapons are better at short range and for keeping enemies from fleeing, particularly in combination with some form of jump denial, and can help your ships survive. They're a useful utility component that would be reasonable to add to just about any ship, with the only drawback being that they're a separate research branch from any weapon system other than graviton beams.
Given I've increased Phaser damage, Phasers should be more balanced now, in which case the Phaser/Beams combination is of limited value.
Phaser/Blaster still ought to have superior DPS to pure phaser and superior armor penetration to pure blaster, if the numbers given in the original post are the numbers you're using. While exactly how much of an improvement over either it will be depends on the exact mix used and on the targets engaged, I don't know that I'd call that 'limited value.' 1.01 DPS per unit size on the Phaser Lance III is still a lot less than the DPS of the Titan Beam II at anything less than 350 range, and given that blaster damage is unchanged, blasters still have a bit of trouble against armor at long range.
It's also not particularly more research intensive than missile/missile bomber/fighter, nor is it like every species would need to use it.