It's tough, I tend to balance them more on a case-by-case basis. Here's the idiot guideline I use, since I like personalizing PrCs to my players and this has come up pretty often.
A quick rule of thumb is to pretend it's a 10-level PrC where the odd levels give the abilities of the original class and the evens give the new stuff. 10-level PrCs just seem to be easier to balance, probably because there are so many of them out there.
In a lot of ways a 5-level PrC is better than this (since you have more room for multiple PrCs, you don't have to wait as long for the good abilities, etc.). On the other hand, PrCs with better HD, skill points, or class skill lists than the original class benefit from being 10 levels.
So, let's say we have a PrC, the Defenders of Bob, intended for Fighters. The class increases skill points to 4+INT per level, and gives these abilities by level:
1> Find Bob
2> Defend Bob I
3> Might of Bob
4> Defend Bob II
5> Invulnerable Bob
So, to make the 10-level version, Defender of Fred, would be:
1> Fighter Bonus Feat
2> Find Fred
3> (nothing)
4> Defend Fred I
5> Fighter Bonus Feat
6> Might of Fred
7> (nothing)
8> Defend Fred II
9> Fighter Bonus Feat
10> Invulnerable Fred
So which is better, a Fighter 5/Fred 10, or a Fighter 10/Bob 5? The Fred has more skill points, and they have the same class abilities. On the other hand, the Bob could have gone Fighter 5/Bob 5/Moose 5, so he has more flexibility.
If the PrC doesn't give any kind of skill point, hit point, BAB, save, class skill, etc. increase, then the 5-level class is better. You can compensate for this by making the prerequisites a bit tougher, so that you enter the 5-level later. For example, maybe a level 5 Fighter can enter Fred, but to reach Bob you have to be level 8. Forcing you to spend 3 more levels in your core class is a substantial penalty, nicely offsetting the added flexibility.
So, to take your 5-level class and convert it to a 10-level, make the prerequisites a bit easier. One less Feat, a few less skill ranks; basically, make it able to be reached 2-3 levels earlier.
For caster-types it's even easier, since you just give "+1 spellcasting level" on the odd levels.