I use Pokesav or PokeGen for IVs mainly for one-time Pokemon (Legendaries, Events, special ones, etc.) or if I want to make up a competitive team in-game. I try to do it legit when I can, but I have so little free time nowadays that I have little choice unless I want to get way too little done each day...
http://nightsbeta09.deviantart.com/ I'm also a Let's Player on YouTube! I LP my favorite games! http://www.youtube.com/user/BetaNights
The only time I use it is for nicknaming Pokemon for which I no longer have the save data or those from previous gens that I want to keep. Also resetting EV's or assigning them to Pokemon which are hard to train (Wobbuffet). I'd rather not poke in my Pokemon's (pun....) data in case I mess up and lose the ability to transfer that Pokemon or use it online.
I also use it to check IV's to see if I have breed or captured useful Pokemon.