Here is how I plan a PC out.
0.) Discuss with the DM what he will/won't allow. Saves me headaches later. This can be done at any point thats confortable for you (I usually do it around step 3).
1.) Decide what role I want to fill in the game (basher, healer, tank, scout, trapsmith, blaster, sage, buffer, or socialite. You can fill more than one). Lets say I choose buffer.
2.) Decide what base class (1-20) level would work best for the idea. (Buffers typically are bards, clerics, wizards, marshals or dragon shaman.) This part might be tempered by what everyone else is playing. I choose bard.
3.) Check and see if there are any feats/PrCs/Spells that accomplish my goal. A Quick perusal shows many good bard-aligned PrCs. I choose virtuoso (an old standby). I also see that I want Song of the Heart from Eberron and Subsonics from Complete Adventurer. I'll leave other feats to choice later.
4.) Map out Pre-Reqs. Figure out what skills I need to start taking ranks in, what feats I'll need, and any other pre-reqs I'll need to have. I'll also note when is the earliest I can get said feats/prcs, but not necessarily when I'll take them.
5.) Quickly note Bab and Save Changes. If your BAB or a save bonus jumps tracks (lower or higher) recalculate what it will be 1, 5, and 10 levels into the PrC. This might make adjustments to ability scores, skills, and feats (no need to be a rapier expert if virtuoso gives you a poor bab).
6.) Finish character gen (if not done already) by rolling/assigning scores, race, and alignment (within guidelines of PrC, if any).
6a.) Check out spells (esp for spontaneous casters) and list a few "wants" and "must haves" for each level. Be ready to swap out a few ideas for later. (We're always getting pounded? Maybe take Cure Mod Wounds rather than eagle's splendor).
7.) Submit for DM approval.