Helium-3 was trapped in the planet when it formed.  Some He is being added by meteoric dust, primarily collecting on the bottom of oceans (although due to subduction, all oceanic tectonic plates are younger than continental plates). However, He will be degassed from oceanic sediment during subduction, so cosmogenic He is not affecting the concentration or noble gas ratios of the mantle.
Helium-3 is created by cosmic ray bombardment, and by lithium spallation reactions which generally occur in the crust. Lithium spallation is the process by which a high-energy neutron bombards a lithium atom, creating a He  and a He ion. This requires significant lithium to adversely affect the He/He ratio.
All degassed helium is lost to space eventually, due to the average speed of helium exceeding the escape velocity for the Earth. Thus, it is assumed the helium content and ratios of Earth's atmosphere have remained essentially stable.
It has been observed that He is present in volcano emissions and oceanic ridge samples.  How He is stored in the planet is under investigation, but it is associated with the mantle and is used as a marker of material of deep origin.
Due to similarities in helium and carbon in magma chemistry, outgassing of helium requires the loss of volatile components (water, carbon dioxide) from the mantle, which happens at depths of less than 60 km. However, He is transported to the surface primarily trapped in the crystal lattice of minerals within fluid inclusions.
Helium-4 is created by radiogenic production (by decay of uranium/thorium-series elements).  The continental crust has become enriched with those elements relative to the mantle and thus more He is produced in the crust than in the mantle.
The ratio (R) of He to He  is often used to represent He  content.  R usually is given as a multiple of the present atmospheric ratio (Ra).
Common values for R/Ra:
* Old continental crust: less than 1
* mid-ocean ridge basalt (MORB): 7 to 9
* Spreading ridge rocks: 9.1 plus or minus 3.6
* Hotspot rocks: 5 to 42
* Ocean and terrestrial water: 1
* Sedimentary formation water: less than 1
* Thermal spring water: 3 to 11
He/He isotope chemistry is being used to date groundwaters, estimate groundwater flow rates, track water pollution, and provide insights into hydrothermal processes, igneous geology and ore genesis. 
* [http://www.geotrack.com.au/uthhe/u-th-he-techinfo.htm (U-Th)/He dating of apatite as a thermal history tool]
* [https://web.archive.org/web/20050210172919/http://lvo.wr.usgs.gov/helium.html USGS: Helium Discharge at Mammoth Mountain Fumarole (MMF)]