The connector family you're looking for is quite tough to track down because it's made by many different companies under various brand names. The good news is that I've been using these in numbers for a long time and have done all the research.
I think the one you're looking for, i.e. those cheap things often found connecting the power switch/HDD LED to a mainboard is called "Mini-PV". Mini-PV has had various owners over the years, i.e. DuPont Connector Systems, Berg Electronics, and is currently owned by FCI as "Mini PV Basics"
Mouser, Farnell, Digi-Key and the rest all stock Genuine Mini-PV (i.e. manufactured by FCI) but this often isn't particularly cost efficient.
eBay knock offs. Search for (DuPont connector) there's heaps up there. You may have to do a few purchases to get a set of decent quality terminals/housings but the expenditure will still be low.
Reputable alternatives. Farnell sell some pretty good "own brand" Mini-PV knock-offs under the series "2226" - they're 100% mechanically compatible with the original FCI parts. The catalogue number for Farnell's own brand terminal is 1593529 (2226TG) http://uk.farnell.com/multicomp/2226tg/crimp-terminal-24-28awg/dp/1593529?Ntt=2226TG.
Heck. Just buy the original parts. I've noticed that the plastic in Genuine FCI connectors a lot more durable than the knock offs making them a lot easier to re-use, in particular, the tab which holds the terminal in is much less likely to snap off.
The male terminal, which is very useful for breadboard work, is unlikely to be found in any catalogues because it wasn't ever officially part of the Mini-PV range, as it is not designed to be a wire-to-wire connector system. eBay looks to be the only option here at present.
This is a bit of a tricky one. Unlike Molex terminals where you can fork out £200 for an amazing performing ergonomic tool, no such options exist for Mini-PV. There's a few tools out there, none particularly ideal for cost or practical reasons.
FCI HT-95 ($$$)
The official way is with FCI's HT-95 (sometimes listed as HT-0095). This tool costs a bank balance busting £1300 (USD 1700). I own this tool, it's good, but is it £1300 good? I'm not sure sure about that. It's quite clumsy to use and is easy to break its jaws during crimping and this tends to cost £100+ to repair each time. For the average hobbyist, forget it.
HT208A & HT213A ($$) These two tools are the historic official crimping tools and sometimes appear on eBay inexpensively. HT208A does larger wires (24AWG) and HT213A does fine wires (28AWG). I own both of them and if you can get one that doesn't have a busted jaw and is complete (i.e. has it's contact locator intact) then they're much better than HT-95 but repairing a busted jaw costs £250+. Overall though, I don't recommend either of these for casual use because finding a good one isn't easy.
Foehrenbach RCY21208 & RCY21213 ($) I've never used either of these tools but they appear to be a sensible contemporary option for a hobbyist who's got a bit of spare cash and would be a good investment for someone who does a lot of Mini-PV. Expect to be stiffed €300ish for these tools. RCY21213 does finer (28AWG) wire and is the only one you'd likely need. RCY21208 does 24AWG wire which is pretty big stuff, overkill for most applications using this type of connector.
Engineer PA-09 (Cheap) By far the most inexpensive crimping tool. Its jaw isn't particularly suited to crimping Mini-PV contacts and it does a bit of a messy job but I suspect the average hobbyist isn't likely to mind very much. Although this tool isn't great for Mini-PV it's very useful for a lot of other contacts and is worth owning for Hobbyists on a budget.
Other options (?) There is another likely Chinese made tool out there which does most of the crimping of Mini-PV, I can tell because every contact I've examined is crimped identically but distinctively different to what I see come out of HT-95 and HT2xxA but thus far I have not managed to identify it.
Crimping quirks As the Male terminal is unofficial, none of the official crimping tools will accept one. It's not impossible to modify an offical tool (As I have done) to accept male terminals, but a far easier option is to use a cheap tool like PA-09 where you can crimp whatever you please.
Noteworthy compatible connector systems
Molex CGRID III A series which is less common but close (Mates with Mini PV and is easy to obtain)
I wouldn't recommend CGRID III because while they will mate with Mini-PV, the contacts and housings are a Molex design and are not interchangeable with Mini-PV i.e. you can't stuff CGRID III terminals in a Mini-PV housing and vice versa.
Having said that though, CGRID III is a lot more robust and features a fantastic Molex branded crimp tool which like all Molex crimp tools, is a dream to use.
TE .100 AMPMODU These appear to be a very similar design to CGRID III but I wouldn't count on any terminal interchangeability with anything.
Even more options
All the big guys: AMP/Tyco/TE Connectivity, Amphenol, JST etc have all produced a plethora of 2.54mm pitch connectors over the years all of which mate with Mini-PV but these are even less common, more expensive and once again, you'll end up having contact/housing compatibility problems so I'd say stick with Mini-PV or Molex CGRID III.
The crimp tools for the remaining options typically always run to four figures.