A robust skill system is important for any game system I'd like to run. I like having an obvious thing that I can ask players to throw out a check for when they describe an action. The older 1e version of making ability checks felt ad hoc and non-robust to me. I also like skill systems as a tool for character definition and differentiation. It says a surprising amount about the character Ricardo Murcielago, for example, that he has a rank or two in Craft (Needlepoint), because his lace always has to look nice, even when he's out in the middle of nowhere without access to a seamstress.
By the same token, though, skills that tread in each other's territory or otherwise feel superfluous or extraneous don't help either. After poking around with various post 3.5 skill systems, and looking at them next to each other (Trailblazer, Pathfinder, Star Wars SAGA and even 4e) I've decided to adopt Pathfinder's skill system wholesale as the easiest of the bunch to integrate into a 3.5 game without having to do much in the way of actual work to convert.
So, while one or two skills do in fact need to be relearned, mostly all you need to do is match up your 3.5 skill to the corresponding Pathfinder skill, and off you go. If you're playing a custom class that has access to Hide and Move Silently, for instance, that class would now have access to Stealth, the single skill that replaces those redundant skills.
The following little chart should highlight the correspondances. If there's no change to the skill, it will be labeled as such. Unless otherwise noted, the rules don't actually change, though. If you want to make a Hide check, you now roll against the Stealth skill, but everything else about making the check is unchanged.
The only skills that require further explanation (which I'll provide another time in a separate post) are Linguistics and Knowledge.
D&D 3.5 Skill::Pathfinder skill
• Appraise::No change
• Balance::Now use Acrobatics
• Bluff::No change
• Climb::No change
• Concentration::Now is a caster level check plus ability modifier of main spellcasting ability
• Craft::No change
• Decipher Script::Now is part of the Linguistics skill
• Diplomacy::No change
• Disable Device::No change
• Disguise::No change
• Escape Artist::No change
• Forgery::Now use the Linguistics skill; read details
• Gather Information::Now use the Diplomacy skill
• Handle Animal::No change
• Heal::No change
• Hide::Now use the Stealth skill
• Intimidate::No change
• Jump::Now use the Acrobatics skill
• Knowledge::More codified with several specific Knowledge skills instead of the vague 3.5 options
• Listen::Now use the Perception skill
• Move Silently::Now use the Stealth skill
• Open Lock::Now use the Disable Device skill
• Perform::No change
• Profession::No change
• Ride::No change
• Search::Now use the Perception skill
• Sense Motive::No change
• Sleight of Hand::No change
• Speak Languages::Now use the Linguistics skill; read details
• Spellcraft::No change
• Spot::Now use the Perception skill
• Survival::No change
• Swim::No change
• Tumble::Now use the Acrobatics skill
• Use Magic Device::No change
• Use Rope::DM will adjudicate skill check, based on situation
The other notable change to the rules from 3.5 is that no character may have skill ranks higher than his character level. HOWEVER, any skill for which a character has at least one rank, and which is a class skill for that character will recieve a +3 bonus to the check result. Note: this also means that characters do not get their skill bonus x4 at first level; they get their skill bonus... x1.