Well you need a full team (Coders, Mappers, Modellers/Skinners, 2D Artists/Spriters, Animators, Sound Artists, Webmasters and don't forget those betatesters :]) unless you can do those by yourself.
Then you need a leader who will motivate the team to do the work. They all have to know what they are doing and one program does not make a mod. A leader has to be kind yet demanding (this is a free modification, they are allowed to quit and have nothing to lose so making it enjoyable is what motivates team members, remember there is no money in this). That's why being a good leader is a tough job, although some leaders can't do any HL Editing, having the ability to do that is still very crutial to a mod.
As a coder, you need some sort of C++ program (or just use wordpad/notepad and a free compiler like Borland). C++ is a language that needs to be learned, so you can't really just step in and start coding awesome mods. You need to download the HL SDK (found at
www.valve-erc.com) and replace the Half-Life code with your own (or some people make mods based on Half-Life so some weapons are kept).
Mappers use Valve Hammer Editor (found at
www.valve-erc.com). I wouldn't say it is the hardest thing in the world to become a mapper but it takes a great deal of practise to become great at it.
Modellers/Skinners use Milkshape3D (found at
www.milkshape3d.com) to make the models and an art program to make the skin (I don't know the skinning process so there might be more to this). As like mapping (since I don't model) I think that anyone can model but to model great takes practise.
2D Artists/Spriters use programs like SprWizard (to turn .bmp's into .spr's), Photoshop or any other form of art program to make the .bmp. They also have to be able to turn .bmp's (made by art programs like stated above) and use the program Wally to turn them into usuable textures for the mapper. The also have the job of making menu's and other jobs the leader has for him/her.
Animators, like Modellers, also use Milkshape3D (found at
www.milkshape3d.com) to animate models, I think this takes skill and patience (lots of patience), anyone can make animations but as DT proves, to be amazing it takes practise.
Sound Artists (yes FreeDom we couldn't forget about you!!!) have the job of adding cool effects and key sounds in order to make your mod have that proffessional feel. I do not know what programs are needed here, but I can assume maybe 3 or so to gather and convert the sounds to .wav's or .mp3's if need.
Then you need a webmaster. This guy is very underestimated because a good looking site can mean the difference of getting those fans to click on forums and sign up or just thinking: "This mod sucks ass". Plus you are going to need hosting ([offtopic]Yay SoulStriker for the hosting and both him and Lost for that kick ass site!!![/offtopic]) so that you can keep your mod organized and even more proffessional. You can get hosting at
www.oktagon.net for cheap hosting on sites and game servers (go Greg).
Ah, the all so eager testers. These are people who follow your mod and you think can critique the mod well and find those potential bugs so that you have a safe final product. These guys should be serious when it comes to testing but still bring the lighter side to mods that team members at times don't have because they are concentrated by their work (you can still have fun teammates but sometimes things can get rough so you need guys like Magus to give you that boost [offtopic]*Magus gets off knees*

Magus!!!).
I think the modellers in ESF either used Milkshape3D, Gmax or 3DS Max. All in all, unless you can do most of the things above (if you want to do one by yourself, all of them) you are going to need a team of people and it can be very hard to find candidates, especially ones that are motivated to do work. But if you can pick up one or more of these and find someone else who can do the rest, then you can pull a Counter-Strike and have two people making a published mod. But making a mod is definately not a cake walk, trust me, it is hard work. Doing it by yourself is almost impossible unless you are very good at all of the above, but who knows, you may pull it off. And if you do, I'll be in the first row with a sign saying: "I told him how to do this".
Some Other Useful Programs
SprView (Used by mappers or sprite artists to view their sprites)
Half-Life Model Viewer (To view skins and animations of your models) [Find it at:
www.milkshape3d.com]
Probably more but it is late so... I'm off...
Thanks for listening to my dollar and a half
[Edit
Wow I went on a rant and totally missed your questions (well not all but most). Well to make beams look in ESF's alpha SDK found in one of the stickies within the Coding/Bug Report Section of these forums.
And if you want to know how they got started go to the ESF fansite (I don't have the URL but if the guy wants to step in here and provide it, go for it). Right now, I think I speak for people that have been here a long time, that they just have a dedicated team that are amazing at what they do. I think any team member would be the first to admit that they couldn't do it without any of the other team members doing their job. That's what a team is supposed to be after all, a group of people working together to accomplish a goal. I think they have long passed their expectations, who could imagine that the forums would be this packed (though members don't seem to stay) for this long.
/Edit]