Skills are one of the big ones, I think, especially things that will get Stealth and/or Perception - since those are two and three separate skills in 3.5 respectively, that'll leave the monsters with a lot of spare skill points left over (presuming they had ranks in all component skills of course) to be reallocated. The simplest method is to just ignore the extra points, but if you so desire you can always shuffle them away into another appropriate skill.
The other is feats, as they're granted at every even HD rather than every third; this is generally a bit simpler, as you just count up their HD and find out how many feats they should have then add in feats for the slots they're missing.
Don't forget the final step of comparing them to stats given in monster desing table at the end of the Bestiary. This is just to check if the monster isn't overpowered or underpowered for its CR and just add a few tweaks to make it fit.
Remember that those rules are guidelines and not hardrules and plenty of monsters break this rules, the hydra has more offense but lower defenses, giants have extra HP and sometimes damage extra damage but lower AC, etc.
Humbly,
Yawar
Remember that certain creature types changed their BAB/HD/Saving Throws/Skills (at the moment I am sure about Constructs, Outsiders and Undead).
BAB is tied to HD (1/level - d10, except Dragons which get d12, .75/level - d8, .5/level - d6).
Elementals are Outsider subtype now. Giants are Humanoid type.
Skill work differently - as was already mentioned many skills were merged with others. Both class and non-class skills cost 1 point per rank with max number of ranks equal to level/HD, increasing values of non-class skills greatly.
Personally I prefer to rebuild 3.0/3.5 creatures from scratch using ability scores and either HD or CR, depending on individual monster. For example, in case of mind flayer I went with HD getting a creature with lower CR than old illithid (to keep with new CR I had turned extract into ability drain caused during maintaining grapple).
Living creatures heal teir level for night sleep, twice for full day rest and twice with heal skill aid, stack with full day rest for a for times your level total.
Their is a table in the gamemastery chapter of the core rules that says how much treasure and encounter should have depending on their CR, standard treasure means they get said amount, this amount is also adjusted by the power level set by the GM (low fantasy, highfantasy, epic fantasy) and the level advancement rate (slow, medium, fast). Its a bit complicated to explain it here, so better read the reward part of the chapter.
Humbly,
Yawar