surge proctector with a higher joule rating or UPS with a lower joule rating?

You are talking apples and oranges.  A surge protector, helps but is not a 100% surge protector item.  Unless you buy a high dollar model (e.g.  a commercial model) there's no guarantee it will really work when needed.  There is a lot of hype in the advertising for these items.  

A UPS on the other hand, provides surge protection plus battery and AC power backup.  You don't want to lose power in the middle of a recording session or even mixing or whatever.  True Sonar will backup at the interval you set, but a sudden power failure with the PC running and you could corrupt the hard drive and lose everything.  Thus the UPS system is the most logical AC power source system.

How much of a UPS you need depends on your power requirements and how long you want your system to run on backup.  I worked in computers and networking management and studies have found that most AC power failures are either momentary or very brief - and that is where the UPS shines and takes care of.  A UPS that will deliver approx 10 minutes of battery power to the PC would take care of the momentary's and also allow you to do an orderly shutdown of the system on a prolonged AC outage. 

In the networking compter room that I used to manage we had a large UPS system (300KVA at 480 VAC) for the entire room that would run for approx 10 and at the 5 minute mark, if we were still on battery our backup AC power generators would start up and sync with the AC power line and if we were still on backup at the 10 minute mark they would automatically go on line.  I know this is overkill for a studio or home PC system - but it shows what the computer industry does.

Finally, the other consideration on a UPS is the power supply in your PC.  New PC's are coming with the "Active PFC" power supplies.  Some of these will only work with "true sine wave" (on battery backup) output UPS systems and some will work with a standard stepped (pseudo sine wave) output UPS provided the switching time is 4Ms or less. 

Bottom line, the only real solution for PC's is a UPS.   I also use a UPS on my new HD TV for AC power line protection.

I'd also like to add that APC makes good ones. The first one I got was Cyber Power and, well, let's just say "uninterrupted" was not an accurate description. :(

A UPS is the way to go. I agree about the brown outs and blinks.... they can really screw up the computer hard drive.

You can have a blink in the middle of a beautiful day, and the UPS also provides a good level of surge protection.  The bigger the wattage rating the better you are.... but even a small UPS will allow you enough time to shutdown the computer in an orderly manner.

The APS I have on this machine has "Parachute software" installed and the UPS actually talks with the computer and in case of a power failure, it determines the battery standby and shuts the computer down if I'm out of the room.

It's hit and miss on whether a specific Active PFC power supply needs the pure sine wave or will work with SOME non pure sine wave model UPS'.   

There was a huge thread on the Dell users forum about this, as new Dell's (desktops) come with Active PFC power supplies.  Most have found they need the true sine wave type units.  However, a few reported they could use a standard pseudo sine wave UPS if the switching time (from AC power line to backup battery) was less than 4ms.  

Bottom line there is no 100% way of telling whether a particular power supply will or will not work with a "standard" UPS system - whether APC, Cyberpower or whatever make.  The ONLY sure way is to connect it to whatever UPS you want to use and then simulate an AC power failure (disconnect the UPS from the AC receptacle) and if the PC continues to run it's OK with that model.   With this in mind, I would only buy a UPS from somewhere that had a liberal return policy so I could return it if it didn't work with my Active PFC power supply.

To muddle things further (grin), I have a 750 watt XFX Active PFC power supply in my home built PC.  I have an older Dell badged APC power supply (was originally sold for business use, not home use) and it works fine.