I have been running a Pathfinder campaign for two years and have used plenty of 3e and 3.5e adventures in it as well as native Pathfinder ones. (I've used multiple adventures from the Atlas Games Penumbra series, Green Ronin Freeport series, Goodman Games Wicked Fantasy Factory series, and older Paizo 3.5e APs and Pathfinder Modules.)
The short form is that 3e monsters/encounters count as CR (or EL)-2, and 3.5e ones count as CR (or EL)-1. In other words, you need a CR 8 3e monster or NPC to provide the punch a CR 6 one does in Pathfinder.
Besides that, you can do as much conversion as you want, but you really don't have to do any. Just run adventures higher in the range band - "D&D 3e for levels 3-5" means use on level 3 characters max unless you want to do conversion work.
My general process when using old ed adventures and actually converting is:
Convert major NPCs. This is where you get the largest differential, and you want your "bosses" to shine; it's not just hit points and attack bonuses but the cool new feats and classes and whatnot you want them to benefit from. I usually use Hero Lab to do NPC builds. (Many of the 3.5e Paizo APs have had fan conversions to Pathfinder posted on the Paizo forums.) My level 4 PCs can dogpile the heck out of a level 8 NPC boss if they're not done up well.
Sub in monsters where they exist in PF. Simple. Just look them up in the Bestiary(/2/3) and use those stats instead.
For lesser NPCs and monsters, either use tougher ones, more of them, or give them a quickie advanced template (or heck, just boost their hit points). For lesser NPCs, if you have the NPC Guide or Gamemastery Guide, there are a bunch of great NPC builds of various levels you can use for normal guards/bandits/soldiers/pirates/townsfolk/etc. and reskin as needed.
And that's it! I don't have the patience to do more, and unless you're publishing it there's no reason to.
Here are a few things to consider :
Tactics
If a full attack is "all" it takes to down someone, force Move actions. Could come from cover/concealment or combat maneuvers like Trip/Knockdown or Disarm. If you just play "rocket tag", you're implicitly accepting that if you miss, there's a good chance you're dead.
Note that this is exactly what happens IRL between powerful forces in a battle and in this respect, is not a "bug" of the system but a simple truth.
Intelligence
So you're targeted by a Master Ninja, who manages to sneak up on you and place a Death attack. Curse you, Hayabusa ! Wait, you made your save ! Time to grab your trusty bow and fill him with arrows...
Well, boo. The ninja has broken/stolen your bow as well. Not only does he make his escape, he's slowed you down by forcing you to have it repaired / replaced while you try to get it back.
This goes a step further in Tactics, and is to be expected of Ninja, for example. Study your target. Know their strengths and weaknesses as well as yours. "That Brilliant Bow of Badassitude could be a problem if I must escape. Can I get rid of it ? What about impairing the bowman ? Maybe I could blind him ?"
As an aside, the GM should make sure the players don't feel cheated though. Extreme competence is assumed as part of the characters (especially past level 10) and robbing them of that can be frustrating to no end for some.
Numbers
So they can take the Big-Ass-Monster down in a round ? What about 10 Medium-Sized-Nuisances ? One by itself could barely hope to hit them, but with flanking, teamwork feats and simply being all over the place, the little pests could prove to be annoying. Add in a Leader-type and you could even be worrying your characters.
Story happens
Take the characters down a notch or two through Story. Have them stripped of Rank and Privileges by the King or even make them straight Outlaws. Have them stranded on an island (and some of their equipment lost to the sea) after their boat got caught in a storm. Have their home base attacked (and their Mentor killed, leaving them unable to progress in their main class) while they were on mission.
Change focus for a while
Once all is said and done, if the combat has become so easy it's boring, it may be time to try a little courtly intrigue for a change. Or why not a mystery ? Possibly meshing with "Story happens" above, there are plenty of opportunities to take the players / characters out of their comfort zone while staying true to the setting. They'll be happy to resume bashing heads once they've stumbled for hours finding a tangible threat to pounce on. Or hey, maybe they'll actually enjoy trading piques with the Jester and decide they want a piece of land and a throne of their own ?
Best Answer
Here's a few considerations:
Version Conflicts
Pathfinder has a lot of small, subtle edits to things like feats, spells, and items that make them function very differently from how they were in 3.5; some of these changes were good, others were, in my opinion, terrible, but in either case you/your group will need to decide what version of each thing you decide to use. The easiest thing to do is decide on a case-by-case basis, but that may or may not be workable or desirable for your group. Another solution I've seen is to use mostly one game (say, PF) and hold the material in that game's Core as being "higher", then adapt supplements as needed. Some things that might have version conflicts:
The Skills Changed
This is technically a sub-set of the above, but it really deserves its own mention because it reaches further. The entire way skills work in PF changed, including some skills becoming parts of others, the class skill/cross-class skill system changing, and even some subtle changes to how skill ranks work. This can affect feat and prestige class pre-requisites, but also how characters meet skill DCs in modules and adventures. Keep it in mind! A side note: Concentration didn't get rolled into another skill, it vanished entirely to become part of the combat system, so you'll need to find something to replace it for Tome of Battle content and/or spellcaster prestige class pre-reqs.
Archetypes
Pathfinder introduced a ton of Archetypes, which are expansions on 3.5's idea of Alternate Class Features. 3.5 content wasn't necessarily designed with these archetypes in mind - likewise, Pathfinder content wasn't necessarily designed with ACFs in mind. Archetypes and ACFs are both great resources to bring a character concept to life (or snatch at fleeting trails of power), but you should decide if you can combine the two ideas or not.
Pathfinder's Feats are Weaker
Almost without exception, non-magical feats in Pathfinder are weaker (often significantly weaker) than 3.5's, to the point where the extra feats Pathfinder hands out still end up with melee being weaker than ever before (more on that in a minute). Does that mean you should enable 3.5 feats gained at the Pathfinder rate? Eh, maybe. If you notice that spellcasters are dominating your game and making it difficult for other party members to contribute, I'd certainly give that a try. Magical feats are just as strong as ever (more on that later), so you may want to extend that benefit just to melee classes.
Pathfinder Content is Biased
More specifically, they're biased towards spellcasters and well away from melee. 3.5 content is also recognizably biased in this fashion, but I do not exaggerate when I state that in Pathfinder's case, Paizo found a way to make the problem even worse. In almost all cases where there's content conflict for melee between 3.5 and Pathfinder, the Pathfinder content is weaker, costs more resources, or both (a wonderful case-in-point is Improved Trip). Likewise, Pathfinder's spellcasters are natively stronger than 3.5s; in addition to their spells (which remain the most powerful, versatile, and changeable resource in the game) they were granted Real Actual Class Features (like the Sorcerer bloodlines), access to in-house metamagic reducers, and suffered no nerfs to their metamagic and other related feats, like Extra Spells Known. On the whole, spellcasters have less "trap" options and more powerful ones than anyone else. Though this is a general balance concern that all groups eventually address, I bring it up to make perfectly clear that Pathfinder excaberated this problem instead of solving it.
And a side note:
Don't Fix it if it Ain't Broke
If your group hasn't experienced one of the problems I have above, don't worry about it. If you're good at eyeballing quick rules references, you don't have to re-write the rulebook. The idea here is to have fun, and I doubt sitting down and writing a comprehensive conversion guide for your group is fun. My personal suggestion is to make a general statement ("PHB is standard, ask about PF content" or something similar) and then handle other issues on a case-by-case basis.
Don't Go to the Paizo Forums for Help
The culture there tends to be very hostile to conversion attempts; that is, the posters and design team (who remain active on their forums) are very invested in Pathfinder and don't appreciate posters asking how they can "dilute" Pathfinder with legacy content.