Here are listed some unusual and rare Devee Devtaa temples.

Asht-Vinaayak Temple
Prominent among the temples of Ganesh are a cluster of eight temples popularly known as Asht Vinaayak temples which are totally dedicated to Shree Mahaa Ganapati. These temples are very ancient where Vinaayak had manifested in different cosmic ages. They are,
(1) Shree Mayooreshwar at Moregaon
(2) Shree Siddhi Vinaayak at Siddhatek
(3) Shree Ballaleshwar at Pali
(4) Shree Varad Vinaayak at Mahad
(5) Shree Chintaamani at Theur
(6) Shree Girijaatmaj at Lenyadri
(7) Shree Vighneshwar at Ozhar
(8) Shree Mahaa Ganapati at Ranjangaon
All these eight temples are located in the state of Mahaarashtra within a radius of about 100 km from Pune city. It is not possible to cover all these temples visit within one day. It requires minimum two or three days for a complete visit. Conducted tour facilities are available from Pune as well as from Mumbai cities. Total distance coverage from Pune will be around 650 km and from Mumbai it will be around 750 km.

Bharat's Temple
The Koodalmaanikyam Temple in Iringalakuda, Trissur district in the state of Kerala is the only temple of Bharat in India. It holds the Deity Bharat as a sage, not as a prince. There are four ponds that are located in and around the temple. The largest of the four are Kuttan Kulam, located outside the compound on the Eastern side, and Kulipini Teertham, located inside the compound.

Dash Mahaavidyaa Temple
Situated in Bhojpur, 30 km from Bhopaal in Madhya Pradesh, "Nikhildham" is a rare place of worship. It is the only temple in India dedicated to the ‘Dasa Mahavidya’ or the ‘Ten Mahavidyaa’. Most temples have one deity or a few deities, but a place of worship dedicated to all the Mahaavidyaa is rare. Nikhil Dhaam was inaugurated in March 2005. Spread over five acres, the temple has the idols of all the Ten Mahavidyaa, specially carved by inspired artisans of Raajasthaan. Nikhildham is home to numerous trees, herbs and hrubs, which are rare and unique for pure Tantra Saadhanaa. The complex is serene and situated on the bank of a river. It is a unique place in the world of spirituality. You may look at the photos at : http://www.dasamahavidhyasadhakparivar.org/photo.html

Dattaatreya Temple
There is a Girnaar Hill, in Joonaa Garh area of Gujaraat, where a famous temple of Dattaatreya is there. One has to climb 10,000 stairs to reach there. People do this climbing overnight and have his Darshan. It is on the way to Somnaath Jyotirling if one is traveling by train. The hill can be seen with steps going up , there was a white colored monument.

Dhanvantari Temple
Maruthurvattam. It is a place near Cherthala and is famous for its Dhanvantari Temple there. This place got the name so because the Vaidyan Moos from Kottaayaam stayed there in olden days and he used to give medicines only once, the diseases used to get cured. The Moos Vaidyan became very famous and patients from far of places started coming to see him. He used to say to those patients coming from distance to their query "Marunnu oru vattam Mathi" - that prescribed medicines are sufficient. Repetition of the medicines for a 2nd time is not needed. As days went on the Moos Vaidyan got famous as Marunnu Oruvattom Vaidyan. The place got the name Marunnu Oruvattam and later it got shortened to "Maruthoor Vattaam" (Read from the legend about Maruthoor Vattam Temple from the Temple website)

Gokarnaatheshwar Temple
Mangalore, Karnaatak.

Maatrikaa Temples
There are two Maatrikaa's Temples - Sapt / Ashta Maatrikaa Temples in Kerala at Kodungallur and Ameda. In both these temples the main deities are Maatrikaa.

Mallikaarjun Temple
Taken from  - A Blog

The Mallikaarjun Temple in Basaraalu is one of the typical Hoysala Temples. It was built by one Harihar Naayak who was the commander in chief under the Hoysala King Raajaa Imaadi Narasimha. The Temple is built in a typical Hosyala style with the base being star shaped. The carvings depict various stories from the Mahaabhaarat in the Puraan. The place is maintained well by the ASI.

The temple has a beautiful Dravidian Shikhar on its main Garbh Griha, which houses a “Balahari Shiv Linga” and a beautiful lotus on the ceiling . The two small Garbh Griha facing each other, house a “Naag Naagin” sculpture in one and the “Soorya Dev” (Sun god) in the other. The vestibule has the symbol of Hoysala, Sala killing a lion. Photography is not allowed inside the sanctum scrotum.

Mallikaarjua Temple, of Basaralu, was built in 13th Century AD, and it can be reached from Bangalore -> Mysore highway -> Mandya ->Take right to Chick Mandya -> then take Left to Basaralu - total distance is about 80 miles (130 Kms)  Overall road conditions are all right.

Narasinh Temple
(1) There is a pillar, believed to be the pillar of appearance of Narasinh Bhagavaan to kill Hiranyakshyap, in Dhaaraadh village, in Poornea District in Bihaar. A big temple of Narasinh Bhagavaan exists behind the same pillar.

(2) There is one temple more in Mahaaraashtra, near the banks of River Krishna, in Sangalee District. It is underground and one has to literally crawl down to reach the inside to witness the  beautiful stone carved sculptured Narasinh and Lakshmee.

Nava Narasinh Temple
See also  Nava Narasinh Kshetra
Here is a travelogue to Nava Narasinh Temple, also called "Dakshin Ahobilam" at Avaniyapuram near Vandavasi / Cheyyar:    http://shanthiraju.wordpress.com/2009/04/28/avaniyapuram/

Patanjali Temple
The world's first temple dedicated to Patanjali was inaugurated by His Holiness Shree Shree Yogaachaarya B.K.S. Iyengar in his holy birthplace of Belloor, a village in Karnaatak, South India, on the 31st October 2004. Patanjali was the son of the Divine Yoginee Gonikaa and is the Divine Expounder of Yog as taught by Kapil Jee (the primordial Holy Incarnation of Vishnu, son of Rishi Kardam and Devahooti)

Saraswatee Temples
(1) There is one Saraswatee Temple in Koothanur in Tanjaavur district (Tamilnaadu).
(2) There is an important Saraswatee Temple in Basar at a distance of 40 km from Nizaamaabaad, in Aadilaabaad District, Aandhra Pradesh on the banks of Godaavaree River.

Seetaa Samaahit Temple
The Seetaa Samaahit Temple stands exactly on the mound where Seetaa Jee descended into Earth. Within the campus of the main temple there exists temples of Seetaa Jee and Shiv Jee. There also stands a 108 feet high statue of Hanuman Jee, the tallest statue of Hanumaan, installed on an artificial rock of 20 feet high. Under this hillock there is a cave having a small temple of Hanumaan Jee. Seetaamarhi is a historical place of immense significance and is being visited by large number of pilgrims with great faith and devotion. It is one of the five Teerth (holy places) in Poorvaanchal - (1) Prayaag, (2) Seetaamarhi, (3) Saarnaath. (4) Vindhyavaasinee and (5) Kaashee, all can be visited within 3 days.

How to reach? It is situated almost midway from Allahabad and Vaaraanasiee. Jangiganj and Bheeti are situated on the GT Road (NH-2 also known as Sher Shah Suri Marg) from where roads lead to Seetamarhi. It is 13 Kms from Jangeeganj and just 7 Kms from Bheeti. One can get bus or taxi from Gopeeganj* - an important town between Allahabad and Vaaraanasee. Allahabad is an important Railway Junction and all trains arrive here from all directions, while Vaaraanasee finds an important place on the air map also.

Shiv, Vishnu and Brahmaa Temple (1)
http://shanthiraju.wordpress.com/2011/04/20/kodumudi/
This Temple is located in a beautiful location with Kaaveree flowing in front at Kodumudi. It is one of the very few temples which enshrines all the three Moorti - Brahmaa, Vishnu and Shiv in exclusive shrines with legendary significance. It is a highly popular Parihaar Sthal for all types of problems. There is a holy and mystic Vannee Tree which is said to be 3000 years old It is a living tree with one side of the tree having thorns and the other side without it. This is the place where river Kaaveree was relieved of her curse of Sage Agastya from his Kamandal. The river which flows Southward from Karnaatak, turns 90 degrees in front of the temple and flows Eastward from here. It is one of the 275 important Shiv temples glorified by Thevara hymns. Sundarar composed his Namachivaaya Patikam here. Saint Arunagirinathar sung "Thirupugazh" on Lord Muruga Kaarttikeya or Skand or Kumaar) of this temple.

Shiv, Vishnu and Brahmaa Temple (2)
There is yet another shrine, perhaps 1000 years old, in a village called Nallur, Tamilnaaadu), 10 KMs from Kumbaakonam, on the way to Vallangaiman, where all three Moorti - Brahmaa, Vishnu and Shiv give Darshan to devotees. This temple is known as Dakshin Kailaash. Where Shiv was married to Paarvatee and marriage rituals were performed by Brahmaa, and Kannigadhanam by Vishnu. There is a Swaayambhu Ling which changes color five times in a day and known as Panch Aavarneshwar. Lot more is written in Sthal Puraan about this famous temple.
[Lot of spiritual significance about the Temple and you can google it for more details - under Nallur, near Kumbaakonam or Panchavarneswarar]

Trivikram Temples
There are only 2 Temples of Trivikram in India. One installed by Brahmaa Jee near Tirukoilur and another one installed by Vaadiraaj at Sodhe.

Varun Dev Temple
A Varun Dev Temple is located in Manoraa Island in Karaachee, Sindh, Paakistaan. The Temple is devoted to Varun, the god of the oceans. The exact year of the Temple's construction or foundation is not known (it may be thousands of years old) but it is widely believed that the current structure was built in around 1917–18. Today, the temple is in a dilapidated state as humid winds are destroying into the structure and the rich carvings on the walls of the temple are slowly eroding. At present, the building is not used for worship and the last ritual was held in the 1950s. Currently, this temple belongs to the Hindu Council of Paakistaan. According to a legend, it was around 16th century when a wealthy sailor by the name of Bhojomal Nancy Bhattia bought Manora Island from the Khan of Kalat, who owned most of the land along the coastline at that time and then his family commissioned a temple on the lay terrain.