I would look into the Lee Filter Foundation Kit, based on the needs you specified. Lee makes a very solid, and less bulky, filter system similar to Cokin's, and it will more than adequately accommodate your need for LOTS of ND filtration, 100mm filters, graduated neutral density, and if you don't mind spending the money, glass and high quality glass (rather than resin) filters also in the 100mm (4x4) format.
I think the Lee filter system is a bit more expensive than the alternatives, like Cokin's, however its pretty versatile. I've been using it for a couple years now, and it was one of my best purchases for landscape photography. The filter holder is completely customizable, so you can adjust it down to hold only one filter or up to 4, and if you need the ability to independently rotate different sets of filters (i.e. one set of ND/GND and one containing a polarizer), you can use the tandem adapter to connect two holders together with independent rotation. That, combined with their circular filter holder and custom hoods, and you have one of the most flexible filter systems on earth. Its a breeze to use, too...the whole filter holder contraption, along with whatever you may have attached to it, clips on and off in one swift little motion, making it easy to meter unfiltered exposure, add the filters again, and take a shot without messing with composition, focus, etc.
Lee offers more filters than I've ever browsed through, as well...including all the important ones: Neutral Density & Graduated Neutral Density (both hard and soft) on .3, .6, .9 and 1.2 (1, 2, 3, and 4 stop) variants, Colored and Graduated Colored filters (really only necessary for film...there is a HUGE variety of these), Glass Linear and Circular Polarizers, even the 10 stop "Big Stopper....a single filter ND filter designed for those extreme exposure scenarios lasting minutes (only problem is it is EXTREMELY hard to find in stock...I've been after it for a year, and still haven't seen it available at any time I've looked, however its been insisted on multiple occasions that they are available and in stock at times...its just in high demand with not enough supply.) All of the 100mm Singh-Ray filters are compatible, although some may need shim adjustment in the Lee mount if they are too thick or thin (which, conveniently, is possible...the Lee filter mount is amazingly flexible, and can take filters from 1mm to 4mm thick.)
While versatile, there are a couple of key drawbacks with Lee filters: the price and availability. Price-wise, it can be expensive. The best way to start is to get one of the starter kits, which usually comes with the mount capable of holding three 100mm (4x4") filters, some kind of solid ND, a hard edge 4x6" ND grad (probably .6/2 stop, but there are a variety of kits), and a filter pouch. That will probably run your around US$200-300. The filter holder runs about US$90 on its own. You'll also need an adapter ring for each filter thread size, and those tend to run anywhere from about US$40 to US$80 or more for the larger ones. Filter holder parts can be cheap or expensive, depending on what you get. You can expand the filter holder to support four filters at a time with more slide guides, get additional screw lengths to support anywhere from 1-4 filters, replace the 2mm slide guides with 1mm or 4mm ones for filters of differing thickness, buy another filter holder and a tandem adapter to support up to 8 concurrent filters in two sets of 1-4, with independent rotation, etc. This stuff ranges from a few bucks to hundreds of dollars. Filters themselves can cost anywhere from about $50 each to as much as $200 each, depending on whether they are resin, glass, or proglass. The good 4x4 Solid ND glass filters tend to cost about US$170 each, and the resin 4x6 Graduated ND resin filters tend to cost about US$100 each. The CPL is pretty expensive at $300, but it is essentially a universally compatible polarizer, and its nice, high quality, sturdy glass...so its kind of worth it.
Beyond price are the occasional supply problems. Right now actually seems to be a good time to buy...the filter holder (foundation kit), starter kits, and most of the key ND/GND filters seem to be in stock at most of the key providers (B&H, Adorama, etc.) The more specialized items, like polarizers, the Big Stopper, etc. are currently out of stock at most places. It is kind of a hit and miss game with Lee...sometimes there are weeks where trying to get any one of their ND filters is impossible, and it takes weeks more for the product to arrive in stock, after which it tends to sell out VERY quickly. Sometimes its really hard to find adapter rings or kit parts, dashing your plans to expand the filter holder from 3 to 4 filter slots. Many of Lee's filters regularly require 7-14 day shipping periods, and usually ship directly from Lee (which I believe is based in Europe...so US customers tend to pay more for shipping and have to wait even longer.) The supply problems have really been the only negative aspect of owning the Lee filter system. I could care less about the price most of the time, if I could just get a hold of the filters I need (I've been trying to get my hands on the 10-stop Big Stopper ND filter for far beyond too long now...and despite the fact that its mostly my fault for not getting on the ball when I'm notified of it being in stock, its still kind of annoying.)
So, while I highly recommend Lee's filter foundation, it can be a bit of an ordeal outfitting yourself with a decent kit. As an example, here is my landscape kit and roughly what it cost:
Item | Quantity | Price
Foundation Kit | 2 | $165 (one as starter kit)
Tandem Adapter | 1 | $28
Adapter Ring 72mm | 1 | $52
Adapter Ring 77mm | 1 | $60
Adapter Ring 82mm | 1 | $64
GND Soft .3/.6/.9 | 1 | $175
GND Hard .3/.6/.9 | 1 | $175
GND Blender .3 | 1 | $100
GND Hard .6 | 1 | $0 (part of starter kit)
ND 0.3 Glass | 1 | $170
ND 0.6 Glass | 1 | $0 (part of starter kit)
CPL Glass | 1 | $300
Accessories | N | ~$30 (alternate screw lengths, holders, shims, slide guides, etc.)
Rough cost per purchase: ~$100
Time to acquire: 2 years
I am still missing a couple key filters as well, including a Solid ND 0.9, and the 10-stop ND "Big Stopper" (which always seem to be on backorder, out of stock, etc.) Tack those on, and the total price is up to about $1500 for a full "Landscape Photographers Godly Filter Kit w/ Epic 10-Stop ND". ;)
Seems really expensive, although it breaks down to about $63 a month savings, and you really don't have the option to buy it all at once anyway given supply quirks. In the end, once you have the filters and kit parts you need...it should literally last forever. You can adapt the kit to work with pretty much any lens from 105mm filter thread down to 30mm filter thread, probably even smaller than that if you really wanted to. If you really wanted your own vari-ND filter, you could grab the $300 CPL and $150 LPL glass filters (VERY nice, HIGH quality), and have something just as good as if not better than the much-vaunted Singh-Ray VaryND, and usable on every lens you now- or might-possibly-one-day own, regardless of angle of view (excluding any specialty lenses that don't support filters to start with, like say Canon's TS-E 17mm or a fisheye.)