The process goes something like...
Calculate all the base price, casting costs, benefit costs and get a total. Be careful here to use the class with the lowest casting level (i.e. if you use a spell that is 3rd level for a cleric and 4th for a wizard, you would calculate the price using the cleric).
Penalties, one shot use, consumables, etc then reduce this price usually.
Even after you have done all that, then you should take this price and compare it against like priced items in the rule books and adjust as needed using your gut instinct.
Unfortunately, pricing is a bit of an esoteric art - its not a major point against you if you are a little bit out, but is noticed when wildly out.
Also, cheap items (say less then 4,000 gp) tend to get scrutinized more as cheap items are much harder to do.
The PRD page you need to refer to is this one.
Hope it helps.
Or put more generally - how much of the total power is offset by the penalty? Heavy boots that give +2 versus forced movement but -2 to swim probably only get a 5 or 10% discount. Sticky gloves that give a +2 bonus to being disarmed but grant a -2 to all other actions using your hands would probably get a much larger one (50% or more).
tell us what this item is, what you want it to do.
NO! Don't do this! And for the record, I hope your comment about losing Strength a round is just a generalization, because breaking anonymity disqualifies your entry
*regains composure*
There are a few reasons you're not seeing any descriptions for how to calculate an item that causes you to lose Strength every round.
1) That's probably a cursed item. And, for the record, submitting a cursed item will disqualify you, because they're not wondrous items. And, cursed items don't have detailed price-calculation charts because they're not something you normally buy.
2) You're looking for the Other Considerations section of the "Creating a Magic Item" page. See how small it is? Typically that's because you're not going to create an item that's terribly restrictive. A decent rule of thumb is to say 0% for a drawback that doesn't affect you, 10% for a slightly inconvienent, and 30% for a serious one. a 50% discount might only apply if you're not going to be able to use the full effect of the spell you're using - like telekenesis, but only for throwing people/things.
If you want an example of an item that already does this, look at the ring of X-ray vision. Lose 1 Con a round. If you compare it to a raw ring of true seeing you get it worth the same as a ring that can be used 1/day, minus about half - which could be a 30% penalty (only through some things) and a 30% penalty (lose 1 Con each round beyond the limit). The numbers aren't perfect, but it gives you a *very* close value to the item you have there.
As a quick rule of thumb, and for arguments sake, create two values for the item.
Calculate what you think your base price is.
Now pretend instead of subtracting or taking away something, calculate the price as if you were adding it (+1 strength in your example)
NOW
Take the value for the powers you are pretending are benefits, subtract them from the powers you gain.
If you go zero or less, then the negatives of the item outweigh the positives of the item and so no one would want it.
It's a very quick rule of thumb, but gives you a starting point.