Well, the S10 has one of the best regulation circuits of any light in its size and price range (the standard S10 at about $40, titanium notwithstanding). It will handle an RCR123 or an IMR 16340, or a regular CR123a primary cell (non-rechargeable). When using the S10, you don't have to really worry about the battery except for the heat buildup, since it's a very small light with little heat dissipation built in. On that front, if you can still hold the head of the light, it's fine.
On those batteries, essentially they use different chemistries. The standard RCR123 that you'll find (most people like the AW brand, as they're very good cells) use a lithium cobalt oxide cell, which is in itself a rather unsafe chemistry. The majority of those batteries you'll find have protection circuits in them that will keep the cell from overchraging, overdischarging, and from discharging too quickly. Again, the AW brand have those protection circuits, and they work well.
The IMR batteries don't have protection circuits, because in some instances they don't need them. IMR is a bit of an interesting misnomer, since they should me "LMO" for lithium manganese oxide (I think...). It doesn't necessarily mean that the cell is safer, but it is ostensibly a safer, more stable cell chemistry than LiCO, and also offers a much lower internal resistance, which would result in a higher amperage coming out of the battery. These would benefit a light that draws a lot of power very quickly.
Just remember that whenever you see a "16340," that's just referring to the size of the battery. It's the width (16mm) by the length (34mm) and a 0. Similarly a AA size battery is referred to as a 14500 for 14x50mm. They're approximate, as you'll find some batteries are longer or shorter depending on the brand and protection circuits. The size is usually just referring to the cell itself. So, you'll also see 18650 batteries and lights, which are very popular because of the large capacity those batteries have for their relative size.
If you want a quick and easy solution to using Li-ion batteries, I recommend getting AW RCR123s, or the Nitecore brand. They're both very good. Stay away from the "XXXXFire" brands like TrustFire. Surefire is a great brand however, but they only make CR123a batteries, not rechargeables as far as I know. For a charger, I recommend the NiteCore Intellicharger, either the i2 or i4. It's a great charger, charges all types of batteries, and does it all automatically and independently. It detects the type of battery, applies the proper charging method, and stops when it's full. Simple as that. It's a good charger, and it simple. You can find them on Amazon. I use the i4, and it works for Li-ion batteries as well as the NiMH rechargeable Eneloops/Duracells/Energizers. It fits the 16340 size as well as the 18650 size. It really does a lot.
Actually, I have a couple of extra AW RCR123s. If you decide to go the route of Li-ion rechargeables, let me know and I'll send a couple your way on the cheap when you pick up a charger. I bought 4 of them, only need two now since I use AA/14500 lights for the most part.
For more details, give these a read:
http://www.rigcast.com/flashlights/lithium-ion-guide/
http://www.candlepowerforums.com/vb/showthread.php?325456-What-exactly-does-quot-IMR-quot-mean
Edit: If you take a look at Going Gear, you'll find AW batteries, but also ones from EagleTac and XTAR. Those are both very good brands, and while I can't confirm those specific batteries, the 18650 batteries I have from EagleTac use very very good cells and work perfectly.
