[RPG] Players better at dealing damage than taking damage

This is a known tendency of 3.5...

As KRyan correctly points out in his answer, to a certain extent this is just the way 3.5 is. There are many options available to players (Save-or-Die/Save-or-Lose/No-Save-Just-Lose spells, ridiculous amounts of damage like you've seen with your Barbarian PC, etc.) that instantly remove enemies from an encounter.

There aren't a whole lot of options for "soft" defense - there are immunities, there are things like immediate actions that protect you from a given attack, but there aren't a lot of good ways available to players to reduce the impact of incoming attacks (many of the best spells are strictly all-or-nothing; Damage Reduction doesn't scale well enough to be an effective protection, etc.).

Put those two things together, and you get what's often called rocket tag - the two sides trade blows that will end the fight if they land, they do their best to prevent enemy blows from landing, and whoever [fails a save/isn't immune to something/takes a full attack/etc.] first loses.

...but it can be mitigated somewhat, by picking options for your enemies that aren't available/optimal for PCs.

The best way I've found to mitigate this issue is to make enemies who are better at taking/preventing damage and other fight-enders than they are at ending fights. This requires building your enemies much differently than you would if you were building them to be effective PCs. Some tips for this approach:

• Make your enemies immune or highly resistant to the standard encounter-enders. Sufficiently high saves prevent save-or-lose spells from being reliable, but if you want to be sure to prevent rocket tag, you may also want to layer on effects like Death Ward, Freedom of Movement, etc.
• Give your enemies lots of HP. As KRyan says, this isn't enough on its own (it just incentivizes your players to use attacks that don't deal HP damage), but combined with defenses against non-damage attacks, it can result in more uptime in fights.
• Give your enemies immediate action defenses, Contingencies, etc. One-shotting an enemy isn't a very satisfying fight outcome. Using your first one-shot move, having it countered by something like Celerity (SpC), then having your party member use a second powerful attack that lands because you've already burned through the enemy's defenses? Feels more like you've accomplished something, and less like you've trivialized the encounter.
• Have your enemies use lots of attacks that work over time, but not very many encounter-enders. Save-or-suck spells like Bestow Curse, damage-over-time effects like Power Word: Pain (RotD) or Freezing Fog (SpC), battlefield control like Web, grappling opponents (if your PCs aren't immune)...these are all strong options that make the PCs feel like Bad Stuff™ is happening to them, without instantly knocking them out of the encounter entirely.
• Use the terrain to make it harder for your PCs to land encounter-enders. If a competently built pouncing Barbarian lands a full attack on pretty much anything, that thing is going to die. So place obstacles that make it hard for the Barbarian to charge, use enemies that fly if your PCs have trouble with that, use incorporeal enemies that move in and out of walls to force your PCs to use readied action attacks, etc.

But isn't this unfair to PCs who specialize in the options I'm hard-countering?

If you just drop it on your PCs with no warning in a game where they've gotten used to normal enemies, yes.

The reason 3.5 has a tendency toward rocket tag is that PCs (and enemies who work roughly like PCs) are much more effective if they build toward offense than defense. In order to counter this tendency, you have to use enemies who don't work like PCs - enemies who have strong defenses that aren't available to PCs, but at the same time don't use some of the most effective offensive options that PCs do.

This may interfere with your players' enjoyment of the game:

• If they expect enemies to be playing by essentially the same rules they are, then the fact that those enemies are immune to lots of their attacks may strike them as unfair - "If that monster's magically immune this stuff, how come I can't be?" or "I spent all these character resources investing in high save DCs for my spells, and now you're telling me the big bad is immune to everything?"
• ...and the fact that their allegedly powerful enemies don't just kill them with encounter-ending spells that they aren't immune to might ruin their suspension of disbelief - "The evil wizard forced me to tromp through his tower full of Freezing Fog fighting skeletons before getting to him. And it was a cool fight, but Freezing Fog is a 6th level spell. If he could cast 6th level spells, why didn't he just nail me with Irresistable Dance on the first round and call it a day?"

But at the same time, you're the DM. Your enemies don't have to be built using the same toolkit that's available to the players, and there's no rule that says they have to have the same capabilities, or be vulnerable to the same forms of attack.

So, talk to your players! See which is more important to an enjoyable gaming experience for your group: enemies who play by the rules, or fights that last longer than three rounds? If you have players who feel they would be unfairly affected by these sorts of changes (e.g., a Beguiler who will be useless if all important enemies are immune to [mind-affecting] stuff), see if they would be okay with being allowed to rebuild their characters to take them into account, or if they prefer the game in its current form.

Then decide how much of this encounter redesign you want to do, with your players' needs and preferences in mind.

What can your players do?

Finally, to address your last question about what your players can do to mitigate this: nothing, unless you change how their enemies work.

The reason 3.5 tends toward rocket tag is that offensive options are stronger than defensive options in the default game. Thus, the best way for PCs to keep themselves alive is usually to take enemies out of the encounter as quickly as possible. From your question, it sounds like your players are already doing this.

If you want to make defensive options viable for them, you have to change the challenges they face - make it so that taking enemies out of the fight quickly is impossible, and then it's no longer the best way to stay alive. Make it so that enemies use damage-over-time effects or debuffs instead of deadly finishing moves, and healing/defensive buffs (besides the ones that provide immunity to encounter-enders) become stronger.

Your players are already doing the right stuff to stay alive in the kind of game they're in. If you want them to behave differently, you have to change their incentives.