I agree with the sentiments here - I'm disappointed in Apple that they can't get simple Intel graphics to work with monitors that all other machines seem to get along with. I have a solution, not as pricey as the Thunderbolt monitor, but still up there, but I have no choice - I have a Mini for fun and a Windows 7 machine for work - two wireless keyboards/mice, one monitor - I just select a different input on the monitor.
I had all the problems we've all been crazy with across the 71 pages of this thread. Here is where I landed: an ASUS PB278Q WQHD monitor. $700 at Micro Center. 27", and it has VGA, DisplayPort, DVI, and HDMI. All cables are provided as well - nice touch by ASUS. The only con I read anywhere on the web was by c|net in that it does not have USB ports - who cares? Buy a crummy $30 hub.
All connections from the Mini work well, but the kicker is with DisplayPort (and DVI, I think)- it takes the resolution up to 2560x1440 and that's when you get the same clarity as Thunderbolt that they always have a Mini attached to when on display in the retail stores. HDMI works very nicely, but you can only drive 1080p or 1600x900 and it looks odd unless you sit back a bit. The PC with Display Port also is an amazing thing to see.
Unfortunately, after $800 for the base Mini, $80 to max out memory, $200 for a 256GB SSD to make it a speedster, and $700 for a monitor, I guess I should have just got a tricked-out iMac. Oh crap, that thing won't support another machine as a display, they take forever to ship them, and I've heard graphics complaints there too.
Good luck.