There is a list of damage types that tend to be used by different NPC factions on the EvE wiki. It also lists which damage types tend to be most effective against them.
NPC damage Types
The various factions and pirates across New Eden tend to inflict particular damage types over others. The following is a list of the damage types inflicted by different factions
Damage done by NPCs
- Angel Cartel: All types, although mostly kinetic and explosive.
- Amarr Navy: EM and thermal.
- Ammatar Navy: EM and thermal.
- Blood Raiders: EM and thermal.
- Caldari Navy: Kinetic and thermal.
- Centii: EM and thermal.
- Coreli: Kinetic and thermal.
- Corpii: EM and thermal.
- Domination: All types, mostly kinetic and explosive.
- Gallente Navy: Kinetic and thermal.
- Gist: All types, mostly kinetic and explosive.
- Guristas: Kinetic and thermal.
- Khanid: EM and thermal.
- Mercenary: All types.
- Mordu's Legion: Kinetic and thermal.
- Odamian: Kinetic and thermal.
- Pith: Kinetic and thermal.
- Rogue Drones: All types.
- Republic fleet: All types, mostly kinetic and explosive.
- Sansha: EM and thermal.
- Serpentis: Kinetic and thermal.
Best damage to do to NPCs
- Guristas - Kinetic
- Serpentis - Thermal or Kinetic
- Mordu's Legion - Thermal or Kinetic
- Blood Raiders - EM or Thermal
- Sansha - EM or Thermal
- Angel Cartel - Explosive
- Mercenary - Thermal
The more advanced the material, the more money you'll make. Why is this? Because you don't have to MESS with more-processed stuff as much.
If you try, for some reason, to deal in unprocessed stuff like "Aqueous Liquids," you'll be out at the customs office every frickin' day with a hauler, and a load will be worth a few thousand isk at most. Bleah.
Go up one level, and "Water" will be a trip every few days, and it's worth a few hundred isk/unit. We're getting into money.
Process it again and you've got "Coolant" at 10k/ unit, and you're hauling once a week. This is almost practical!
The details can change, but the basic idea applies to everything. I'm working on Robotics, myself, but it's still 1 isk/unit "Heavy Metals" going into 100 isk/unit "Toxic Metals" going into 1000 isk/unit "Mechanical Parts going into 60k/unit Robotics. Same pattern.
One last thought: Think about where you live. What systems are handy to you? What planet types are in those systems? Look at the spreadsheet at https://spreadsheets.google.com/spreadsheet/lv?key=0ArlHEr5t26lndDN3QVhBODJ3YnF5MWVMcUQ0bHdxQXc&f=true&noheader=true&gid=0 . What level-3 commodities can you build by combining only two planets nearby? That's what you build.
Best Answer
There's no best, but similar to other ship classes they provide different bonuses and advantages/disadvantages.
I'm not really sure whether you're referring to the T1 frigates with an exploration bonus or the T2 CovOps frigates, which offer stronger bonuses.
Either way, the short answer is quite simple: Pick the exploration frigate that fits your starting faction, especially if you're new, because this will save you some skill time for now.
The long answer (as well as long-time answer): It depends on personal preferrance.
Which one to pick? Up to you. While exploration frigates are often untanked (they're more about avoiding fights or getting away before being shot), some tank fitting your skills won't necessarily hurt. Despite that, you'll usually need at least two medium powered slots for your exploration modules. Keeping that in mind three out of four frigates can be a good choice, with the Magnate having a slight disadvantage.
Their T2 counterparts, Anathema, Buzzard, Helios, and Cheetah further build on these strengths and weaknesses (although with some shifted focus, e.g. the Cheetah being an armor tanked ship and only the Helios is able to field a single light drone).
EVE Online: Rubicon also introduced the Astero as a new exploration frigate provided by the *Sisters of Eve** faction. Although having similar exploration bonuses, this ship isn't really recommended for new players. It requires multiple skill lines to master (e.g. Amarr Frigate as well as Gallente Frigate, Small Energy Turrets as well as drone skills) and it's not really cheap to obtain.
If you'd like to read more about exploration as introduced with EVE Online: Odyssey as well as starter tips and more details about the different ships being available, you can have a look at this article on the EVE University's wiki.