I'm a big fan of Tomato, used it for many years, but the problem is that it's hampered by using the proprietary wireless drivers and so is stuck on an ancient kernel lacking modern features. Tomato also uses NVRAM to store configuration which is limited to 32KB (60KB on newer devices) which may be an issue if the OP wants to configure it up the wazoo.
If the OP wants to go with a consumer router then i'd recommend something that can run OpenWrt. OpenWrt is a full-fledged embedded Linux distribution with configuration done in text files in the file system (can also be configured by web GUI or command-line UCI
). It uses opensource wireless drivers and comes with a recent kernel (Barrier Breaker currently has 3.10.44).
If "N" wireless is sufficient then i'd say the TP-Link WDR4900
is still the best router out there. It uses a powerful PPC processor rather than the weedy MIPS processors most routers use and the processor has crypto extensions which should boost throughput if the OP runs any kind of VPN server on it.
I still think that, for a power-user, the Ubiquiti route is the way to go though.