Like the Napoleonic period the Second World War seems to polarise wargamers by their preferred rule sets. Until relatively recently I had a problem finding any sets of rules that I felt provided the flavour that I was looking for at the various scales you can game the period. I thought I'd outline the rules I've now found and why I like them (you will probably also see full reviews of these rules at various times in the future - indeed I have reviewed one of them already). This isn't to say that other WW2 rules are bad but simply that I prefer these (and as you will see there is still a gap I am trying to fill). You may notice my list doesn't include Rapid Fire, I'm not a big fan of these rules generally as I think they play like a skirmish but as that's not the level they are trying to represent that's not a plus point! However, I would agree that they are relatively simple to pick up and might be a good introduction to the period. Anyway here are my favourites:
Nuts! from Two Hour Wargames is the WW2 variant of their Chain Reaction 2 skirmish rules.
The chain reaction concept takes a little while to get your head around but once mastered I find it provides the best modern skirmish games I have ever played. It neatly represents the feeling of a fire fight and the effect of troop quality and leadership very well. The rules provide both the basic game mechanics for infantry, armour and artillery along with army lists (though focussed on mid to late war) and a campaign system. It's a great package based on an excellent series of mechanics that give a great skirmish game.
I Ain't Been Shot, Mum from the Too Fat Lardies has been reviewed by me before and whilst also at a 1:1 ratio uses the section as the basic manouevre unit.
The use of an interrupted card based initiative system and reducing action dice generates a series of challenges for the player acting at a Company commander level or higher. It works as both a two player and multi-player level and the rules are easy to pick up and play.
The fact that not every unit can act every turn can be a little frustrating at first but it does present a very interesting series of challenges to the player. Obviously for multi-player games it is essential that the distribution of units is properly thought through to avoid prolonged downtime.
My final selection is Great Battles of World War II by Bruce McFarlane (originally published by The Canadian Wargamers Group). These rules use a company as their smallest manouevre unit and allow the player to operate at a Brigade or Division commander level.
The rules are designed around fighting large multi-day actions as units gradually grind to a halt during combat and have to be reorganised overnight. A Divisional Centre of Operations and Forming Up Place are represented and provide reference points for deployment and lines of communication and supply.
The CWG rules sets include background, rules and scenarios as a complete package and the original two volumes were The Canadians in Europe and Dropzone which dealt with major airbourne campaigns (Crete and Market Garden). A third early war volume (Invasion '40) has also been released and is available, along with a .pdf version of the rules as part of the CWP offering at Saber's Edge Hobbies & Games (whose website appears to be down at the moment).
The obvious omission from this list is a set of rules at Regimental level. I have used Spearhead for this but, whilst a decent set of rules, I'm afraid they don't float my boat.