Before I dig into your list of lights, I'm going to point out that in order to go rechargeable on all of them, you will pretty much have to have 3 different rechargeable chemistries and 3 different chargers to get the best results in all areas. I'll list the 3 chemistries you will want to look into having to run everything, then go into what goes where to the best of my ability.
1. 1.2V NIMH rechargable cells: In various common sizes (AA, C, D etc), these you are probably already familiar with so I won't say too much more on this subject. Investment in a good multibay smart charger like a MAHA 808 is highly recommended if you are going to accumulate a number of NIMH cells for various devices. I also highly recomend owning nothing but Low-Self-Discharge cells, like eneloops in AA, and LSD Accupower cells in C and D sizes.
2. 3.7V Lithium Cobalt Oxide (LiCoO2): This is what we are talking about most of the time when we say lithium ion. This is what AWs li-ion cells are, and is what the WF-139 will charge. Make sure you get a WF-139 with the spacers for charging RCR123s, all other sizes you have listed will fit without the need for spacers. As a side note, a RCR123, is equivalent to a 16340 size cell. If you can afford it, I would suggest a Pila IBC charger. It is a more robust charger with better quality charging characteristics. The WF-139 will overcharge cells if you leave them on the charger. AWs protected cells are the best value IMO.
3. 3.0V Lithium Iron Phosphate: The chemistry of these cells is almost always indicated in the description or name as "LiFeP04" . These are a semi-new breed of cell. They have substancially lower overall power density than the li-ion described in "2" above, but they have some distinct advantages: they are closer to the operating voltage of CR123 primary cells, so can often act as direct replacements for CR123 primaries in devices that don't tolerate the higher voltage of LiCoO2 cells. they are "safe" chemistry cells, they can be abused, overcharged, over-discharged, overheated, punctured, smashed, etc, without much risk of flame or explosion. There are some LiCoO2 cells out there with voltage reducing diodes built in to have an output closer to 3.0V like the LiFeP04 and CR123 primary cells, but the problem there, is the protection/voltage regulation all adds components that can fail. The simplicity of the LiFeP04 cell, even though it has less capacity, is often worth the tradeoff for it's reliability. I suggest a kit like this for simplicity sake:
http://www.batteryjunction.com/2rc375reliba.html add extra cells to the order if needed.
.....However, for flashlights, or configurations that can tolerate the higher voltage of LiCoO2 cells, I still recommend high quality protected 3.7V cells...
Gladius: 2 3.0V LiFeP04 RCR123 cells is a good solution. I have read of people using pairs of 3.7V cells in these, but I don't think it is good for the light, someone correct me if I am wrong here.
SF E1e+KL1: I think you can run a 3.7V RCR123 here, however, it will overdrive it to the tune of, well, a lot brighter than stock, as I understand it, when the input voltage rises above the Vf of the the configuration, it just goes into direct drive. Get confirmation on this before attempting as I am not 100% sure on this. I am pretty much 100% sure you can use a 3.0V LiFeP04 RCR123 in this configuration to maintain close to stock operation, but with shorter runtime.
SF E2e+KL4: I think the most common method here is to use a single 3.7V 17670 size LiCoO2 cell, someone correct me if I am wrong.
(on a side note, I believe you could put the KL4 on the E1E and run a 3.7V RCR123 in the E1E for a more compact, albeit shorter running little pocket rocket)
SF G3: A Pair of 17500 size 3.7V cells for the P90, or any lamp up to and including the LumensFactory EO-9. Do not run the P91 on 17500s as it is above the maximum safe discharge rate.
G2L: A pair of 3.7V RCR123 will work fine if you want flat regulated output at it's maximum possible output with reduced runtime. A single 3.7V 17670 will also work well, but will have tapering off output but very extended runtime compared with the 2 RCR123s.
9P+LED+FM34+Z49: assuming by "LED" here you mean the surefire LED drop-in, in which case, a pair of 3.7V 17500s is a perfect replacement.
Fenix L2T: 2 AA size 1.2V NIMH
P1DCE: 3.0V LiFeP04 RCR123 cell.
P2DCE: 3.0V LiFeP04 RCR123 cell.
P3DCE: 2 3.7V RCR123s.
L2DCE: 2 1.2V NIMH AAs.
P2D R100: 3.0V LiFeP04 RCR123 cell.
P3D R100: 2 3.7V RCR123s.
T1 SMO: Pretty sure it's compatible with 2 3.7V RCR123s.
Mini-Mag AA+TerraLux 5WLED: Assuming NIMH AAs here?
Mag 2D+TerraLux 5WLED: probably NIMH Ds
6D 'Skull Basher: NIMH Ds I'm thinkin..
LumaPower M3 Transformer + turbo head: You can run it on 1x NIMH AA, 2x NIMH AA, 1 3.7V 14500 or 1x 3.7V RCR123.
Gerber Sonic: NIMH AAA