I've done the HQ thing a few times over the years. The trick to pulling it off successfully is to make it colorful and fun and ultimately not really give the PCs a net gain. If a side business is attached (its a keep with taxable peasants around, its a tavern, an import/export business, etc) make income barely exceed overhead, just as with most businesses. The PCs might gain a bit of gold per month but that might not even exceed their 'lifestyle' expenses (room/board, food, mundane equipment restocking, etc). The PCs, generally, don't want a keep or HQ to exploit the game and make mad money. They want it for the coolness factor. So give them what they want. Such things are a great source for adventure hooks and adventures centered around their ownership (competing with rivals, border disputes, marauding monsters, thieves, corrupt government interference, etc). And it really does help tie the PCs to the setting. They own a piece of it, now, and will go to great lengths to defend it.
My last two campaigns as a DM both featured bases. The older one had the PCs come into ownership of a large three story building with storage facilities in a large city. They formed an adventuring company to gain local status, opened a bar in the front, and ran an import/export business out of the back. The PCs weren't often directly involved with the day to day administration, they hired people for that. But they had a place to unwind, a source of income, a home, and a great source of adventure.
The last one, the PCs decided to claim a crumbling keep they cleared in a dangerous forest. It was actually a drain on their resources, rather than any kind of boon. It definitely put the ruin in ruin and they had to start sinking money into it to make it livable (construction, hireling, taxes, etc). But it was theirs and they loved it. They had also acquired an elemental powered land cart that they mounted a couple everlasting wands on, basically creating a military jeep out of it. So, in effect, they had the Eberron dream - a house and a car. Good times.